mirror of https://github.com/lammps/lammps.git
Merge branch 'collected-small-changes' into reset-command
This commit is contained in:
Axel Kohlmeyer
commit
4ba604fd37
|
|
@ -31,7 +31,6 @@ table above.
|
|||
* :doc:`bond_style <bond_style>`
|
||||
* :doc:`bond_write <bond_write>`
|
||||
* :doc:`boundary <boundary>`
|
||||
* :doc:`box <box>`
|
||||
* :doc:`change_box <change_box>`
|
||||
* :doc:`clear <clear>`
|
||||
* :doc:`comm_modify <comm_modify>`
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@ Setup simulation box:
|
|||
:columns: 4
|
||||
|
||||
* :doc:`boundary <boundary>`
|
||||
* :doc:`box <box>`
|
||||
* :doc:`change_box <change_box>`
|
||||
* :doc:`create_box <create_box>`
|
||||
* :doc:`dimension <dimension>`
|
||||
|
|
|
|||
|
|
@ -2,10 +2,11 @@ Removed commands and packages
|
|||
=============================
|
||||
|
||||
This page lists LAMMPS commands and packages that have been removed from
|
||||
the distribution and provides suggestions for alternatives or replacements.
|
||||
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
|
||||
print a suitable error message in most cases, when a style/command is used
|
||||
that has been removed.
|
||||
the distribution and provides suggestions for alternatives or
|
||||
replacements. LAMMPS has special dummy styles implemented, that will
|
||||
stop LAMMPS and print a suitable error message in most cases, when a
|
||||
style/command is used that has been removed or will replace the command
|
||||
with the direct alternative (if available) and print a warning.
|
||||
|
||||
Fix ave/spatial and fix ave/spatial/sphere
|
||||
------------------------------------------
|
||||
|
|
@ -17,6 +18,14 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
|
|||
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
|
||||
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
|
||||
|
||||
Box command
|
||||
-----------
|
||||
|
||||
.. deprecated:: TBD
|
||||
|
||||
The *box* command has been removed and the LAMMPS code changed so it won't
|
||||
be needed. If present, LAMMPS will ignore the command and print a warning.
|
||||
|
||||
Reset_ids, reset_atom_ids, reset_mol_ids commands
|
||||
-------------------------------------------------
|
||||
|
||||
|
|
|
|||
|
|
@ -144,11 +144,6 @@ does not change the atom positions due to non-periodicity. In this
|
|||
mode, if you tilt the system to extreme angles, the simulation will
|
||||
simply become inefficient, due to the highly skewed simulation box.
|
||||
|
||||
The limitation on not creating a simulation box with a tilt factor
|
||||
skewing the box more than half the distance of the parallel box length
|
||||
can be overridden via the :doc:`box <box>` command. Setting the *tilt*
|
||||
keyword to *large* allows any tilt factors to be specified.
|
||||
|
||||
Box flips that may occur using the :doc:`fix deform <fix_deform>` or
|
||||
:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
|
||||
option with either of the commands.
|
||||
|
|
|
|||
|
|
@ -262,6 +262,8 @@ Disable generating a citation reminder (see above) at all.
|
|||
|
||||
**-nonbuf**
|
||||
|
||||
.. versionadded:: 15Sep2022
|
||||
|
||||
Turn off buffering for screen and logfile output. For performance
|
||||
reasons, output to the screen and logfile is usually buffered, i.e.
|
||||
output is only written to a file if its buffer - typically 4096 bytes -
|
||||
|
|
|
|||
|
|
@ -25,23 +25,25 @@ The *gaussian* angle style uses the potential:
|
|||
|
||||
.. math::
|
||||
|
||||
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
|
||||
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right)
|
||||
|
||||
This analytical form is a suitable potential for obtaining mesoscale
|
||||
effective force fields which can reproduce target atomistic
|
||||
distributions :ref:`(Milano) <Milano1>`.
|
||||
|
||||
This analytical form is a suitable potential for obtaining
|
||||
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
|
||||
The following coefficients must be defined for each angle type via the
|
||||
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* T temperature at which the potential was derived
|
||||
* :math:`T` temperature at which the potential was derived
|
||||
* :math:`n` (integer >=1)
|
||||
* :math:`A_1` (-)
|
||||
* :math:`w_1` (-)
|
||||
* :math:`A_1` (> 0, radians)
|
||||
* :math:`w_1` (> 0, radians)
|
||||
* :math:`\theta_1` (degrees)
|
||||
* ...
|
||||
* :math:`A_n` (-)
|
||||
* :math:`w_n` (-)
|
||||
* :math:`A_n` (> 0, radians)
|
||||
* :math:`w_n` (> 0, radians)
|
||||
* :math:`\theta_n` (degrees)
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -25,33 +25,34 @@ The *gaussian* bond style uses the potential:
|
|||
|
||||
.. math::
|
||||
|
||||
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
|
||||
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right)
|
||||
|
||||
This analytical form is a suitable potential for obtaining
|
||||
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
|
||||
This analytical form is a suitable potential for obtaining mesoscale
|
||||
effective force fields which can reproduce target atomistic
|
||||
distributions :ref:`(Milano) <Milano0>`
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
|
||||
the data file or restart files read by the :doc:`read_data <read_data>`
|
||||
or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
* T temperature at which the potential was derived
|
||||
* :math:`T` temperature at which the potential was derived
|
||||
* :math:`n` (integer >=1)
|
||||
* :math:`A_1` (-)
|
||||
* :math:`w_1` (-)
|
||||
* :math:`r_1` (length)
|
||||
* :math:`A_1` (> 0, distance)
|
||||
* :math:`w_1` (> 0, distance)
|
||||
* :math:`r_1` (>= 0, distance)
|
||||
* ...
|
||||
* :math:`A_n` (-)
|
||||
* :math:`w_n` (-)
|
||||
* :math:`r_n` (length)
|
||||
* :math:`A_n` (> 0, distance)
|
||||
* :math:`w_n` (> 0, distance)
|
||||
* :math:`r_n` (>= 0, distance)
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the
|
||||
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
|
||||
page for more info.
|
||||
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
|
||||
doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
|
|
|||
|
|
@ -1,70 +0,0 @@
|
|||
.. index:: box
|
||||
|
||||
box command
|
||||
===========
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
box keyword value ...
|
||||
|
||||
* one or more keyword/value pairs may be appended
|
||||
* keyword = *tilt*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*tilt* value = *small* or *large*
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
box tilt large
|
||||
box tilt small
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Set attributes of the simulation box.
|
||||
|
||||
For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword
|
||||
allows simulation domains to be created with arbitrary tilt factors,
|
||||
e.g. via the :doc:`create_box <create_box>` or
|
||||
:doc:`read_data <read_data>` commands. Tilt factors determine how
|
||||
skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` page for a discussion of triclinic
|
||||
boxes in LAMMPS.
|
||||
|
||||
LAMMPS normally requires that no tilt factor can skew the box more
|
||||
than half the distance of the parallel box length, which is the first
|
||||
dimension in the tilt factor (x for xz). If *tilt* is set to
|
||||
*small*, which is the default, then an error will be
|
||||
generated if a box is created which exceeds this limit. If *tilt*
|
||||
is set to *large*, then no limit is enforced. You can create
|
||||
a box with any tilt factors you wish.
|
||||
|
||||
Note that if a simulation box has a large tilt factor, LAMMPS will run
|
||||
less efficiently, due to the large volume of communication needed to
|
||||
acquire ghost atoms around a processor's irregular-shaped sub-domain.
|
||||
For extreme values of tilt, LAMMPS may also lose atoms and generate an
|
||||
error.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command cannot be used after the simulation box is defined by a
|
||||
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
|
||||
:doc:`read_restart <read_restart>` command.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
||||
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default value is tilt = small.
|
||||
|
|
@ -13,7 +13,6 @@ Commands
|
|||
bond_style
|
||||
bond_write
|
||||
boundary
|
||||
box
|
||||
change_box
|
||||
clear
|
||||
comm_modify
|
||||
|
|
|
|||
|
|
@ -66,20 +66,21 @@ positive or negative values and are called "tilt factors" because they
|
|||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelepiped.
|
||||
|
||||
By default, a *prism* region used with the create_box command must
|
||||
have tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
|
||||
By default, a *prism* region used with the create_box command must have
|
||||
tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
|
||||
the distance of the parallel box length. For example, if
|
||||
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
|
||||
box length is 10 and the :math:`xy` tilt factor must be between :math:`-5` and
|
||||
:math:`5`. Similarly, both :math:`xz` and :math:`yz` must be between
|
||||
:math:`-(x_\text{hi}-x_\text{lo})/2` and :math:`+(y_\text{hi}-y_\text{lo})/2`.
|
||||
Note that this is not a limitation, since if the maximum tilt factor is 5 (as
|
||||
in this example), then configurations with tilt :math:`= \dots, -15`,
|
||||
:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots`
|
||||
are all geometrically equivalent. If you wish to define a box with tilt
|
||||
factors that exceed these limits, you can use the :doc:`box tilt <box>`
|
||||
command, with a setting of *large*\ ; a setting of *small* is the
|
||||
default.
|
||||
box length is 10 and the :math:`xy` tilt factor must be between
|
||||
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
|
||||
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
|
||||
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this example),
|
||||
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
|
||||
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
|
||||
equivalent. Simulations with large tilt factors will run inefficiently,
|
||||
since they require more ghost atoms and thus more communication. With
|
||||
very large tilt factors, LAMMPS will eventually produce incorrect
|
||||
trajectories and stop with errors due to lost atoms or similar.
|
||||
|
||||
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ Syntax
|
|||
yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
*axes* values = axes length diam = draw xyz axes
|
||||
axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
|
||||
axes = *yes* or *no* = do or do not draw xyz axes lines next to simulation box
|
||||
length = length of axes lines as fraction of respective box lengths
|
||||
diam = diameter of axes lines as fraction of shortest box length
|
||||
*subbox* values = lines diam = draw outline of processor sub-domains
|
||||
|
|
|
|||
|
|
@ -640,7 +640,7 @@ specified by the *max_rxn* keyword.
|
|||
.. versionadded:: TBD
|
||||
|
||||
The *rate_limit* keyword can enforce an upper limit on the overall
|
||||
rate of the reaction. The number of reaction occurences is limited to
|
||||
rate of the reaction. The number of reaction occurrences is limited to
|
||||
Nlimit within an interval of Nsteps timesteps. No reactions are
|
||||
permitted to occur within the first Nsteps timesteps of the first run
|
||||
after reading a data file. Nlimit can be specified with an equal-style
|
||||
|
|
|
|||
|
|
@ -44,19 +44,23 @@ Examples
|
|||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix can be used to simulate non-equilibrium molecular dynamics
|
||||
(NEMD) under diagonal flow fields, including uniaxial and bi-axial
|
||||
flow. Simulations under continuous extensional flow may be carried
|
||||
out for an indefinite amount of time. It is an implementation of the
|
||||
boundary conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
|
||||
These fixes can be used to simulate non-equilibrium molecular dynamics
|
||||
(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow.
|
||||
Simulations under continuous extensional flow may be carried out for an
|
||||
indefinite amount of time. It is an implementation of the boundary
|
||||
conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
|
||||
lattice reduction as was proposed by :ref:`(Hunt) <Hunt>`. The lattice
|
||||
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is intended for
|
||||
simulations of homogeneous flows, and integrates the SLLOD equations
|
||||
of motion, originally proposed by Hoover and Ladd (see :ref:`(Evans and Morriss) <Sllod>`). Additional detail about this implementation can be
|
||||
found in :ref:`(Nicholson and Rutledge) <Nicholson>`.
|
||||
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is
|
||||
intended for simulations of homogeneous flows, and integrates the SLLOD
|
||||
equations of motion, originally proposed by Hoover and Ladd (see
|
||||
:ref:`(Evans and Morriss) <Sllod>`). Additional detail about this
|
||||
implementation can be found in :ref:`(Nicholson and Rutledge)
|
||||
<Nicholson>`.
|
||||
|
||||
Note that NEMD simulations of a continuously strained system can be
|
||||
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>` commands.
|
||||
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
|
||||
<fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
|
||||
commands.
|
||||
|
||||
The applied flow field is set by the *eps* keyword. The values
|
||||
*edot_x* and *edot_y* correspond to the strain rates in the xx and yy
|
||||
|
|
@ -73,11 +77,11 @@ to -(*edot_x* + *edot_y*).
|
|||
The boundary conditions require a simulation box that does not have a
|
||||
consistent alignment relative to the applied flow field. Since LAMMPS
|
||||
utilizes an upper-triangular simulation box, it is not possible to
|
||||
express the evolving simulation box in the same coordinate system as
|
||||
the flow field. This fix keeps track of two coordinate systems: the
|
||||
flow frame, and the upper triangular LAMMPS frame. The coordinate
|
||||
systems are related to each other through the QR decomposition, as is
|
||||
illustrated in the image below.
|
||||
express the evolving simulation box in the same coordinate system as the
|
||||
flow field. These fixes keep track of two coordinate systems: the flow
|
||||
frame, and the upper triangular LAMMPS frame. The coordinate systems are
|
||||
related to each other through the QR decomposition, as is illustrated in
|
||||
the image below.
|
||||
|
||||
.. image:: JPG/uef_frames.jpg
|
||||
:align: center
|
||||
|
|
@ -99,12 +103,12 @@ using the dump command will be in the LAMMPS frame unless the
|
|||
----------
|
||||
|
||||
Temperature control is achieved with the default Nose-Hoover style
|
||||
thermostat documented in :doc:`fix npt <fix_nh>`. When this fix is
|
||||
thermostat documented in :doc:`fix nvt <fix_nh>`. When this fix is
|
||||
active, only the peculiar velocity of each atom is stored, defined as
|
||||
the velocity relative to the streaming velocity. This is in contrast
|
||||
to :doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame
|
||||
velocity, and removes the contribution from the streaming velocity in
|
||||
order to compute the temperature.
|
||||
the velocity relative to the streaming velocity. This is in contrast to
|
||||
:doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame velocity,
|
||||
and removes the contribution from the streaming velocity in order to
|
||||
compute the temperature.
|
||||
|
||||
Pressure control is achieved using the default Nose-Hoover barostat
|
||||
documented in :doc:`fix npt <fix_nh>`. There are two ways to control the
|
||||
|
|
@ -156,8 +160,8 @@ The following commands will not work:
|
|||
|
||||
----------
|
||||
|
||||
These fix computes a temperature and pressure each timestep. To do
|
||||
this, it creates its own computes of style "temp/uef" and
|
||||
These fixes compute a temperature and pressure each timestep. To do
|
||||
this, they create their own computes of style "temp/uef" and
|
||||
"pressure/uef", as if one of these two sets of commands had been
|
||||
issued:
|
||||
|
||||
|
|
@ -169,18 +173,19 @@ issued:
|
|||
compute fix-ID_temp all temp/uef
|
||||
compute fix-ID_press all pressure/uef fix-ID_temp
|
||||
|
||||
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute pressure/uef <compute_pressure_uef>` commands for details. Note
|
||||
that the IDs of the new computes are the fix-ID + underscore + "temp"
|
||||
or fix_ID + underscore + "press".
|
||||
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute
|
||||
pressure/uef <compute_pressure_uef>` commands for details. Note that
|
||||
the IDs of the new computes are the fix-ID + underscore + "temp" or
|
||||
fix_ID + underscore + "press".
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
The fix writes the state of all the thermostat and barostat variables,
|
||||
as well as the cumulative strain applied, to :doc:`binary restart files <restart>`. See the :doc:`read_restart <read_restart>` command
|
||||
for info on how to re-specify a fix in an input script that reads a
|
||||
restart file, so that the operation of the fix continues in an
|
||||
uninterrupted fashion.
|
||||
as well as the cumulative strain applied, to :doc:`binary restart files
|
||||
<restart>`. See the :doc:`read_restart <read_restart>` command for info
|
||||
on how to re-specify a fix in an input script that reads a restart file,
|
||||
so that the operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
@ -189,43 +194,41 @@ uninterrupted fashion.
|
|||
not contain the cumulative applied strain, will this keyword be
|
||||
necessary.
|
||||
|
||||
This fix can be used with the :doc:`fix_modify <fix_modify>` *temp* and
|
||||
*press* options. The temperature and pressure computes used must be of
|
||||
type *temp/uef* and *pressure/uef*\ .
|
||||
These fixes can be used with the :doc:`fix_modify <fix_modify>` *temp*
|
||||
and *press* options. The temperature and pressure computes used must be
|
||||
of type *temp/uef* and *pressure/uef*\ .
|
||||
|
||||
This fix computes the same global scalar and vector quantities as :doc:`fix npt <fix_nh>`.
|
||||
These fixes compute the same global scalar and vector quantities as
|
||||
:doc:`fix nvt andnpt <fix_nh>`.
|
||||
|
||||
The fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
These fixes are not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the UEF package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
These fixes are part of the UEF package. They are only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
Due to requirements of the boundary conditions, when the *strain*
|
||||
keyword is set to zero (or unset), the initial simulation box must be
|
||||
cubic and have style triclinic. If the box is initially of type ortho,
|
||||
use :doc:`change_box <change_box>` before invoking the fix.
|
||||
|
||||
.. note::
|
||||
|
||||
When resuming from restart files, you may need to use :doc:`box tilt
|
||||
large <box>` since LAMMPS has internal criteria from lattice
|
||||
reduction that are not the same as the criteria in the numerical
|
||||
lattice reduction algorithm.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix nvt <fix_nh>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, :doc:`compute temp/uef <compute_temp_uef>`, :doc:`compute pressure/uef <compute_pressure_uef>`, :doc:`dump cfg/uef <dump_cfg_uef>`
|
||||
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
|
||||
:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
|
||||
:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
|
||||
:doc:<dump_cfg_uef>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default keyword values specific to this fix are exy = xyz, strain
|
||||
= 0 0. The remaining defaults are the same as for :doc:`fix npt <fix_nh>`
|
||||
except tchain = 1. The reason for this change is given in
|
||||
The default keyword values specific to these fixes are exy = xyz, strain
|
||||
= 0 0. The remaining defaults are the same as for :doc:`fix nvt or npt
|
||||
<fix_nh>` except tchain = 1. The reason for this change is given in
|
||||
:doc:`fix nvt/sllod <fix_nvt_sllod>`.
|
||||
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -82,7 +82,7 @@ mixing as described below:
|
|||
|
||||
* :math:`\epsilon` = well depth (energy units)
|
||||
* :math:`\sigma` = minimum effective particle radii (distance units)
|
||||
* :math:`\zeta` = tune parameter for the slope of the attractive branch
|
||||
* :math:`\zeta` = tuning parameter for the slope of the attractive branch
|
||||
* :math:`\mu` = parameter related to bending rigidity
|
||||
* :math:`\beta` = parameter related to the spontaneous curvature
|
||||
* cutoff (distance units)
|
||||
|
|
|
|||
|
|
@ -129,6 +129,8 @@ The first argument of the *python* command is either the *source*
|
|||
keyword or the name of a Python function. This defines the mode
|
||||
of the python command.
|
||||
|
||||
.. versionchanged:: TBD
|
||||
|
||||
If the *source* keyword is used, it is followed by either a file name or
|
||||
the *here* keyword. No other keywords can be used. The *here* keyword
|
||||
is followed by a string with python commands, either on a single line
|
||||
|
|
|
|||
|
|
@ -340,16 +340,20 @@ and are called "tilt factors" because they are the amount of
|
|||
displacement applied to faces of an originally orthogonal box to
|
||||
transform it into the parallelepiped.
|
||||
|
||||
By default, the tilt factors (xy,xz,yz) can not skew the box more than
|
||||
half the distance of the corresponding parallel box length. For
|
||||
example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
|
||||
xy tilt factor must be between -5 and 5. Similarly, both xz and yz
|
||||
must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not
|
||||
a limitation, since if the maximum tilt factor is 5 (as in this
|
||||
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
||||
... are all geometrically equivalent. If you wish to define a box
|
||||
with tilt factors that exceed these limits, you can use the :doc:`box tilt <box>` command, with a setting of *large*\ ; a setting of
|
||||
*small* is the default.
|
||||
The tilt factors (xy,xz,yz) should not skew the box more than half the
|
||||
distance of the corresponding parallel box length. For example, if
|
||||
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
|
||||
box length is 10 and the :math:`xy` tilt factor must be between
|
||||
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
|
||||
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
|
||||
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this example),
|
||||
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
|
||||
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
|
||||
equivalent. Simulations with large tilt factors will run inefficiently,
|
||||
since they require more ghost atoms and thus more communication. With
|
||||
very large tilt factors, LAMMPS will eventually produce incorrect
|
||||
trajectories and stop with errors due to lost atoms or similar.
|
||||
|
||||
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
|
|
|
|||
|
|
@ -2360,6 +2360,7 @@ Ng
|
|||
nghost
|
||||
Nghost
|
||||
Ngpu
|
||||
ngpus
|
||||
Ngyuen
|
||||
nh
|
||||
nharmonic
|
||||
|
|
@ -2385,6 +2386,7 @@ nktv
|
|||
nl
|
||||
nlayers
|
||||
nlen
|
||||
Nlimit
|
||||
nlines
|
||||
Nlines
|
||||
nlo
|
||||
|
|
@ -2474,6 +2476,7 @@ nsq
|
|||
Nstart
|
||||
nstats
|
||||
Nstep
|
||||
Nsteps
|
||||
nsteplast
|
||||
Nstop
|
||||
nsub
|
||||
|
|
@ -3091,6 +3094,7 @@ Rutuparna
|
|||
rx
|
||||
rxd
|
||||
rxnave
|
||||
rxnbond
|
||||
rxnsum
|
||||
ry
|
||||
Ryckaert
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.0.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.1.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.0.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.1.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.0.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.1.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -0,0 +1 @@
|
|||
../mols/data.lmp
|
||||
|
|
@ -22,7 +22,7 @@ pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
|
|||
pair_coeff * * sph/rhosum 4.0
|
||||
pair_coeff * * sph/idealgas 0.75 4.0
|
||||
|
||||
compute rhoatom all shp/rho/atom
|
||||
compute rhoatom all sph/rho/atom
|
||||
compute ieatom all sph/e/atom
|
||||
compute esph all reduce sum c_ieatom # total internal energy
|
||||
compute ke all ke
|
||||
|
|
|
|||
|
|
@ -28,8 +28,8 @@
|
|||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define SMAL 0.001
|
||||
#define SMALL 1.0e-8
|
||||
static constexpr double SMALL = 0.001;
|
||||
static constexpr double SMALLG = 2.0e-308;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -112,7 +112,7 @@ void AngleGaussian::compute(int eflag, int vflag)
|
|||
if (c < -1.0) c = -1.0;
|
||||
|
||||
s = sqrt(1.0 - c * c);
|
||||
if (s < SMAL) s = SMAL;
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0 / s;
|
||||
|
||||
// force & energy
|
||||
|
|
@ -123,13 +123,15 @@ void AngleGaussian::compute(int eflag, int vflag)
|
|||
for (int i = 0; i < nterms[type]; i++) {
|
||||
dtheta = theta - theta0[type][i];
|
||||
prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
|
||||
exponent = -2 * dtheta * dtheta / (width[type][i] * width[type][i]);
|
||||
exponent = -2.0 * dtheta * dtheta / (width[type][i] * width[type][i]);
|
||||
g_i = prefactor * exp(exponent);
|
||||
sum_g_i += g_i;
|
||||
sum_numerator += g_i * dtheta / (width[type][i] * width[type][i]);
|
||||
}
|
||||
|
||||
if (sum_g_i < SMALL) sum_g_i = SMALL;
|
||||
// avoid overflow
|
||||
if (sum_g_i < sum_numerator * SMALLG) sum_g_i = sum_numerator * SMALLG;
|
||||
|
||||
if (eflag) eangle = -(force->boltz * angle_temperature[type]) * log(sum_g_i);
|
||||
|
||||
// I should check about the sign of this expression
|
||||
|
|
@ -198,14 +200,16 @@ void AngleGaussian::allocate()
|
|||
|
||||
void AngleGaussian::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (narg < 6) utils::missing_cmd_args(FLERR, "angle_coeff", error);
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
|
||||
|
||||
double angle_temperature_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
int n = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||
if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for angle coefficients");
|
||||
if (n < 1) error->all(FLERR, "Invalid angle style gaussian value for n: {}", n);
|
||||
|
||||
if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "angle_coeff", error);
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
|
|
@ -223,7 +227,9 @@ void AngleGaussian::coeff(int narg, char **arg)
|
|||
theta0[i] = new double[n];
|
||||
for (int j = 0; j < n; j++) {
|
||||
alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
|
||||
if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]);
|
||||
width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
|
||||
if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]);
|
||||
theta0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp) * MY_PI / 180.0;
|
||||
setflag[i] = 1;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@
|
|||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define SMALL 1.0e-10
|
||||
static constexpr double SMALL = 2.0e-308;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -92,15 +92,16 @@ void BondGaussian::compute(int eflag, int vflag)
|
|||
for (int i = 0; i < nterms[type]; i++) {
|
||||
dr = r - r0[type][i];
|
||||
prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
|
||||
exponent = -2 * dr * dr / (width[type][i] * width[type][i]);
|
||||
exponent = -2.0 * dr * dr / (width[type][i] * width[type][i]);
|
||||
g_i = prefactor * exp(exponent);
|
||||
sum_g_i += g_i;
|
||||
sum_numerator += g_i * dr / (width[type][i] * width[type][i]);
|
||||
}
|
||||
|
||||
// force & energy
|
||||
if (sum_g_i < SMALL) sum_g_i = SMALL;
|
||||
// avoid overflow
|
||||
if (sum_g_i < sum_numerator * SMALL) sum_g_i = sum_numerator * SMALL;
|
||||
|
||||
// force & energy
|
||||
if (r > 0.0)
|
||||
fbond = -4.0 * (force->boltz * bond_temperature[type]) * (sum_numerator / sum_g_i) / r;
|
||||
else
|
||||
|
|
@ -153,14 +154,15 @@ void BondGaussian::allocate()
|
|||
|
||||
void BondGaussian::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (narg < 6) utils::missing_cmd_args(FLERR, "bond_coeff", error);
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double bond_temp_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
int n = utils::inumeric(FLERR, arg[2], false, lmp);
|
||||
if (narg != 3 * n + 3) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (n < 1) error->all(FLERR, "Invalid bond style gaussian value for n: {}", n);
|
||||
if (narg != 3 * n + 3) utils::missing_cmd_args(FLERR, "bond_coeff", error);
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
|
|
@ -176,8 +178,11 @@ void BondGaussian::coeff(int narg, char **arg)
|
|||
r0[i] = new double[n];
|
||||
for (int j = 0; j < n; j++) {
|
||||
alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
|
||||
if (alpha[i][j] <= 0.0) error->all(FLERR, "Invalid value for A_{}: {}", j, alpha[i][j]);
|
||||
width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
|
||||
if (width[i][j] <= 0.0) error->all(FLERR, "Invalid value for w_{}: {}", j, width[i][j]);
|
||||
r0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp);
|
||||
if (r0[i][j] <= 0.0) error->all(FLERR, "Invalid value for r0_{}: {}", j, r0[i][j]);
|
||||
setflag[i] = 1;
|
||||
}
|
||||
count++;
|
||||
|
|
|
|||
|
|
@ -18,8 +18,6 @@
|
|||
|
||||
#include "pair_nm_cut.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
|
|
@ -28,6 +26,8 @@
|
|||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
|
|
|||
|
|
@ -223,8 +223,7 @@ void PairNMCutCoulCut::settings(int narg, char **arg)
|
|||
|
||||
void PairNMCutCoulCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6 || narg > 8)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (narg < 6 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
|
|
@ -238,8 +237,8 @@ void PairNMCutCoulCut::coeff(int narg, char **arg)
|
|||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
double cut_coul_one = cut_coul_global;
|
||||
if (narg >= 7) cut_coul_one = cut_lj_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
if (narg == 8) cut_coul_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
if (narg >= 7) cut_coul_one = cut_lj_one = utils::numeric(FLERR,arg[6],false,lmp);
|
||||
if (narg == 8) cut_coul_one = utils::numeric(FLERR,arg[7],false,lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
|
|
|
|||
|
|
@ -277,7 +277,7 @@ void PairNMCutCoulLong::coeff(int narg, char **arg)
|
|||
double mm_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
if (narg == 7) cut_lj_one = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
if (narg == 7) cut_lj_one = utils::numeric(FLERR,arg[6],false,lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
|
|
|
|||
|
|
@ -190,26 +190,34 @@ void ComputeFEP::init()
|
|||
Perturb *pert = &perturb[m];
|
||||
|
||||
pert->ivar = input->variable->find(pert->var);
|
||||
if (pert->ivar < 0) error->all(FLERR, "Variable name for compute fep does not exist");
|
||||
if (pert->ivar < 0)
|
||||
error->all(FLERR, "Variable name {} for compute fep does not exist", pert->var);
|
||||
if (!input->variable->equalstyle(pert->ivar))
|
||||
error->all(FLERR, "Variable for compute fep is of invalid style");
|
||||
error->all(FLERR, "Variable {} for compute fep is of invalid style", pert->var);
|
||||
|
||||
if (force->pair == nullptr) error->all(FLERR, "compute fep pair requires pair interactions");
|
||||
|
||||
if (pert->which == PAIR) {
|
||||
pairflag = 1;
|
||||
Pair *pair = nullptr;
|
||||
if (lmp->suffix_enable) {
|
||||
if (lmp->suffix) {
|
||||
auto pstyle = fmt::format("{}/{}", pert->pstyle, lmp->suffix);
|
||||
pair = force->pair_match(pstyle, 1);
|
||||
}
|
||||
if ((pair == nullptr) && lmp->suffix2) {
|
||||
auto pstyle = fmt::format("{}/{}", pert->pstyle, lmp->suffix2);
|
||||
pair = force->pair_match(pstyle, 1);
|
||||
}
|
||||
}
|
||||
|
||||
if (lmp->suffix_enable)
|
||||
pair = force->pair_match(std::string(pert->pstyle)+"/"+lmp->suffix,1);
|
||||
|
||||
if (pair == nullptr) pair = force->pair_match(pert->pstyle,1);
|
||||
if (pair == nullptr) pair = force->pair_match(pert->pstyle, 1);
|
||||
if (pair == nullptr)
|
||||
error->all(FLERR,
|
||||
"compute fep pair style "
|
||||
"does not exist");
|
||||
error->all(FLERR, "compute fep pair style {} does not exist", pert->pstyle);
|
||||
|
||||
void *ptr = pair->extract(pert->pparam, pert->pdim);
|
||||
if (ptr == nullptr) error->all(FLERR, "compute fep pair style param not supported");
|
||||
if (ptr == nullptr)
|
||||
error->all(FLERR, "compute fep pair style param {} not supported", pert->pparam);
|
||||
|
||||
pert->array = (double **) ptr;
|
||||
|
||||
|
|
|
|||
|
|
@ -96,6 +96,7 @@ PairPACEExtrapolation::PairPACEExtrapolation(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
aceimpl = new ACEALImpl;
|
||||
scale = nullptr;
|
||||
flag_compute_extrapolation_grade = 0;
|
||||
extrapolation_grade_gamma = nullptr;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -51,7 +51,6 @@ class PairPACEExtrapolation : public Pair {
|
|||
|
||||
void allocate();
|
||||
std::vector<std::string> element_names; // list of elements (used by dump pace/extrapolation)
|
||||
int nelements; // # of unique elements
|
||||
double *extrapolation_grade_gamma; //per-atom gamma value
|
||||
|
||||
int flag_compute_extrapolation_grade;
|
||||
|
|
|
|||
|
|
@ -22,6 +22,7 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
|
|||
#include "atom_vec.h"
|
||||
#include "citeme.h"
|
||||
#include "comm.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_bond_history.h"
|
||||
|
|
@ -118,10 +119,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
|
|||
fix3 = nullptr;
|
||||
reset_mol_ids = nullptr;
|
||||
|
||||
if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " "too few arguments");
|
||||
if (narg < 8) utils::missing_cmd_args(FLERR,"fix bond/react", error);
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_size(world,&nprocs);
|
||||
newton_bond = force->newton_bond;
|
||||
|
||||
restart_global = 1;
|
||||
|
|
@ -494,7 +493,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
|
|||
for (int i = 0; i < nreacts; i++) {
|
||||
for (int j = 0; j < nconstraints[i]; j++) {
|
||||
if (constraints[j][i].type == ARRHENIUS) {
|
||||
rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + me);
|
||||
rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + comm->me);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -529,7 +528,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
random = new RanMars*[nreacts];
|
||||
for (int i = 0; i < nreacts; i++) {
|
||||
random[i] = new RanMars(lmp,seed[i] + me);
|
||||
random[i] = new RanMars(lmp,seed[i] + comm->me);
|
||||
}
|
||||
|
||||
// set comm sizes needed by this fix
|
||||
|
|
@ -1251,6 +1250,7 @@ void FixBondReact::close_partner()
|
|||
|
||||
void FixBondReact::superimpose_algorithm()
|
||||
{
|
||||
const int nprocs = comm->nprocs;
|
||||
local_num_mega = 0;
|
||||
ghostly_num_mega = 0;
|
||||
|
||||
|
|
@ -1400,7 +1400,7 @@ void FixBondReact::superimpose_algorithm()
|
|||
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
|
||||
|
||||
int rxnflag = 0;
|
||||
if (me == 0)
|
||||
if (comm->me == 0)
|
||||
for (int i = 0; i < nreacts; i++) {
|
||||
reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
|
||||
rxnflag += reaction_count[i] + ghostly_rxn_count[i];
|
||||
|
|
@ -1440,7 +1440,7 @@ void FixBondReact::superimpose_algorithm()
|
|||
memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts");
|
||||
memory->create(all_localskips,nprocs,"bond/react:all_localskips");
|
||||
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
|
||||
if (me == 0) {
|
||||
if (comm->me == 0) {
|
||||
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
|
||||
// when using variable input for rate_limit, rate_limit_overstep could be > delta_rxn (below)
|
||||
// we need to limit overstep to the number of reactions on this timestep
|
||||
|
|
@ -2615,7 +2615,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
|
|||
}
|
||||
|
||||
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
|
||||
if (me == 0)
|
||||
if (comm->me == 0)
|
||||
for (int i = 0; i < twomol->natoms; i++) {
|
||||
if ((create_atoms[i][myrxn] == 0) &&
|
||||
(twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) &&
|
||||
|
|
@ -2947,6 +2947,7 @@ broadcast entries of mega_glove which contain nonlocal atoms for perusal by all
|
|||
void FixBondReact::ghost_glovecast()
|
||||
{
|
||||
#if !defined(MPI_STUBS)
|
||||
const int nprocs = comm->nprocs;
|
||||
|
||||
global_megasize = 0;
|
||||
|
||||
|
|
@ -2965,7 +2966,7 @@ void FixBondReact::ghost_glovecast()
|
|||
int *allstarts = new int[nprocs];
|
||||
|
||||
int start = 0;
|
||||
for (int i = 0; i < me; i++) {
|
||||
for (int i = 0; i < comm->me; i++) {
|
||||
start += allncols[i];
|
||||
}
|
||||
MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world);
|
||||
|
|
@ -2993,7 +2994,7 @@ void FixBondReact::ghost_glovecast()
|
|||
}
|
||||
}
|
||||
// let's send to root, dedup, then broadcast
|
||||
if (me == 0) {
|
||||
if (comm->me == 0) {
|
||||
MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
|
||||
&(global_mega_glove[0][0]), allncols, allstarts,
|
||||
column, 0, world);
|
||||
|
|
@ -3003,7 +3004,7 @@ void FixBondReact::ghost_glovecast()
|
|||
column, 0, world);
|
||||
}
|
||||
|
||||
if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
|
||||
if (comm->me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
|
||||
MPI_Bcast(&global_megasize,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world);
|
||||
|
||||
|
|
@ -3745,7 +3746,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
|
|||
Superpose3D<double, double **> superposer(n2superpose);
|
||||
int fitroot = 0;
|
||||
if (ifit >= 0 && ifit < atom->nlocal) {
|
||||
fitroot = me;
|
||||
fitroot = comm->me;
|
||||
|
||||
// get 'temperatere' averaged over site, used for created atoms' vels
|
||||
t = get_temperature(my_mega_glove,1,iupdate);
|
||||
|
|
@ -3763,7 +3764,8 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
|
|||
int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
|
||||
if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
|
||||
if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) {
|
||||
error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",me);
|
||||
error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",
|
||||
comm->me);
|
||||
continue;
|
||||
}
|
||||
iatom = atom->map(my_mega_glove[ipre+1][iupdate]);
|
||||
|
|
@ -3791,7 +3793,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
|
|||
if (create_atoms[m][rxnID] == 1) {
|
||||
// apply optimal rotation/translation for created atom coords
|
||||
// also map coords back into simulation box
|
||||
if (fitroot == me) {
|
||||
if (fitroot == comm->me) {
|
||||
MathExtra::matvec(rotmat,twomol->x[m],coords[m]);
|
||||
for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i];
|
||||
imageflags[m] = atom->image[ifit];
|
||||
|
|
@ -3879,7 +3881,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
|
|||
|
||||
int root = 0;
|
||||
if (flag) {
|
||||
root = me;
|
||||
root = comm->me;
|
||||
|
||||
atom->avec->create_atom(twomol->type[m],coords[m]);
|
||||
int n = atom->nlocal - 1;
|
||||
|
|
@ -4025,7 +4027,7 @@ void FixBondReact::read_map_file(int myrxn)
|
|||
while (strlen(keyword)) {
|
||||
if (strcmp(keyword,"InitiatorIDs") == 0 || strcmp(keyword,"BondingIDs") == 0) {
|
||||
if (strcmp(keyword,"BondingIDs") == 0)
|
||||
if (me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead.");
|
||||
if (comm->me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead.");
|
||||
bondflag = 1;
|
||||
readline(line);
|
||||
sscanf(line,"%d",&ibonding[myrxn]);
|
||||
|
|
@ -4291,7 +4293,7 @@ void FixBondReact::open(char *file)
|
|||
void FixBondReact::readline(char *line)
|
||||
{
|
||||
int n;
|
||||
if (me == 0) {
|
||||
if (comm->me == 0) {
|
||||
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
}
|
||||
|
|
@ -4308,7 +4310,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
|
|||
// eof is set to 1 if any read hits end-of-file
|
||||
|
||||
int eof = 0;
|
||||
if (me == 0) {
|
||||
if (comm->me == 0) {
|
||||
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
||||
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
|
||||
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
||||
|
|
@ -4327,7 +4329,7 @@ void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
|
|||
// bcast keyword line to all procs
|
||||
|
||||
int n;
|
||||
if (me == 0) n = strlen(line) + 1;
|
||||
if (comm->me == 0) n = strlen(line) + 1;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
}
|
||||
|
|
@ -4492,7 +4494,7 @@ void FixBondReact::write_restart(FILE *fp)
|
|||
memcpy(rbuf,&store_rxn_count[0][0],sizeof(int)*rbufcount);
|
||||
}
|
||||
|
||||
if (me == 0) {
|
||||
if (comm->me == 0) {
|
||||
int size = nreacts*sizeof(Set)+(rbufcount+1)*sizeof(int);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(&revision,sizeof(int),1,fp);
|
||||
|
|
|
|||
|
|
@ -25,7 +25,6 @@ FixStyle(bond/react,FixBondReact);
|
|||
#define LMP_FIX_BOND_REACT_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "compute.h"
|
||||
|
||||
#include <map>
|
||||
#include <set>
|
||||
|
|
@ -55,7 +54,6 @@ class FixBondReact : public Fix {
|
|||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
int me, nprocs;
|
||||
int newton_bond;
|
||||
int nreacts;
|
||||
int *nevery;
|
||||
|
|
@ -236,7 +234,7 @@ class FixBondReact : public Fix {
|
|||
std::vector<std::string> customvarstrs;
|
||||
int nvvec;
|
||||
double **vvec; // per-atom vector to store custom constraint atom-style variable values
|
||||
Compute *cperbond; // pointer to 'compute bond/local' used by custom constraint ('rxnbond' function)
|
||||
class Compute *cperbond; // pointer to 'compute bond/local' used by custom constraint ('rxnbond' function)
|
||||
std::map<std::set<tagint>, int> atoms2bond; // maps atom pair to index of local bond array
|
||||
std::vector<std::vector<Constraint>> constraints;
|
||||
|
||||
|
|
|
|||
|
|
@ -281,9 +281,7 @@ void ChangeBox::command(int narg, char **arg)
|
|||
} else if (ops[m].style == BOUNDARY) {
|
||||
domain->set_boundary(3,&arg[ops[m].boundindex],1);
|
||||
if (domain->dimension == 2 && domain->zperiodic == 0)
|
||||
error->all(FLERR,
|
||||
"Cannot change box z boundary to "
|
||||
"non-periodic for a 2d simulation");
|
||||
error->all(FLERR, "Cannot change box z boundary to non-periodic for a 2d simulation");
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
|
|
|
|||
|
|
@ -32,6 +32,10 @@ void Deprecated::command(int narg, char **arg)
|
|||
if (cmd == "DEPRECATED") {
|
||||
if (lmp->comm->me == 0) utils::logmesg(lmp, "\nCommand 'DEPRECATED' is a dummy command\n\n");
|
||||
return;
|
||||
} else if (cmd == "box") {
|
||||
if (lmp->comm->me == 0)
|
||||
utils::logmesg(lmp, "\nThe 'box' command has been removed and will be ignored\n\n");
|
||||
return;
|
||||
} else if (utils::strmatch(cmd, "^kim_")) {
|
||||
std::string newcmd("kim");
|
||||
newcmd += " " + cmd.substr(4);
|
||||
|
|
|
|||
|
|
@ -14,6 +14,7 @@
|
|||
#ifdef COMMAND_CLASS
|
||||
// clang-format off
|
||||
CommandStyle(DEPRECATED,Deprecated);
|
||||
CommandStyle(box,Deprecated);
|
||||
CommandStyle(kim_init,Deprecated);
|
||||
CommandStyle(kim_interactions,Deprecated);
|
||||
CommandStyle(kim_param,Deprecated);
|
||||
|
|
|
|||
119
src/domain.cpp
119
src/domain.cpp
|
|
@ -82,7 +82,6 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
|
|||
minzlo = minzhi = 0.0;
|
||||
|
||||
triclinic = 0;
|
||||
tiltsmall = 1;
|
||||
|
||||
boxlo[0] = boxlo[1] = boxlo[2] = -0.5;
|
||||
boxhi[0] = boxhi[1] = boxhi[2] = 0.5;
|
||||
|
|
@ -212,16 +211,13 @@ void Domain::set_initial_box(int expandflag)
|
|||
if (dimension == 2 && (xz != 0.0 || yz != 0.0))
|
||||
error->all(FLERR,"Cannot skew triclinic box in z for 2d simulation");
|
||||
|
||||
// error check or warning on triclinic tilt factors
|
||||
// check on triclinic tilt factors
|
||||
|
||||
if (triclinic) {
|
||||
if ((fabs(xy/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) ||
|
||||
(fabs(xz/(boxhi[0]-boxlo[0])) > 0.5 && xperiodic) ||
|
||||
(fabs(yz/(boxhi[1]-boxlo[1])) > 0.5 && yperiodic)) {
|
||||
if (tiltsmall)
|
||||
error->all(FLERR,"Triclinic box skew is too large");
|
||||
else if (comm->me == 0)
|
||||
error->warning(FLERR,"Triclinic box skew is large");
|
||||
if ((fabs(xy/(boxhi[1]-boxlo[1])) > 0.5 && yperiodic) ||
|
||||
((fabs(xz)+fabs(yz))/(boxhi[2]-boxlo[2]) > 0.5 && zperiodic)) {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Triclinic box skew is large. LAMMPS will run inefficiently.");
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -981,25 +977,33 @@ void Domain::subbox_too_small_check(double thresh)
|
|||
this should not be used if atom has moved infinitely far outside box
|
||||
b/c while could iterate forever
|
||||
e.g. fix shake prediction of new position with highly overlapped atoms
|
||||
use minimum_image_once() instead
|
||||
uses minimum_image_once() instead
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
static constexpr double MAXIMGCOUNT = 16;
|
||||
|
||||
void Domain::minimum_image(double &dx, double &dy, double &dz)
|
||||
{
|
||||
if (triclinic == 0) {
|
||||
if (xperiodic) {
|
||||
if (fabs(dx) > (MAXIMGCOUNT * xprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx);
|
||||
while (fabs(dx) > xprd_half) {
|
||||
if (dx < 0.0) dx += xprd;
|
||||
else dx -= xprd;
|
||||
}
|
||||
}
|
||||
if (yperiodic) {
|
||||
if (fabs(dy) > (MAXIMGCOUNT * yprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy);
|
||||
while (fabs(dy) > yprd_half) {
|
||||
if (dy < 0.0) dy += yprd;
|
||||
else dy -= yprd;
|
||||
}
|
||||
}
|
||||
if (zperiodic) {
|
||||
if (fabs(dz) > (MAXIMGCOUNT * zprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz);
|
||||
while (fabs(dz) > zprd_half) {
|
||||
if (dz < 0.0) dz += zprd;
|
||||
else dz -= zprd;
|
||||
|
|
@ -1008,6 +1012,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
|
|||
|
||||
} else {
|
||||
if (zperiodic) {
|
||||
if (fabs(dz) > (MAXIMGCOUNT * zprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dz);
|
||||
while (fabs(dz) > zprd_half) {
|
||||
if (dz < 0.0) {
|
||||
dz += zprd;
|
||||
|
|
@ -1021,6 +1027,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
|
|||
}
|
||||
}
|
||||
if (yperiodic) {
|
||||
if (fabs(dy) > (MAXIMGCOUNT * yprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dy);
|
||||
while (fabs(dy) > yprd_half) {
|
||||
if (dy < 0.0) {
|
||||
dy += yprd;
|
||||
|
|
@ -1032,6 +1040,8 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
|
|||
}
|
||||
}
|
||||
if (xperiodic) {
|
||||
if (fabs(dx) > (MAXIMGCOUNT * xprd))
|
||||
error->one(FLERR, "Atoms have moved too far apart ({}) for minimum image\n", dx);
|
||||
while (fabs(dx) > xprd_half) {
|
||||
if (dx < 0.0) dx += xprd;
|
||||
else dx -= xprd;
|
||||
|
|
@ -1040,75 +1050,6 @@ void Domain::minimum_image(double &dx, double &dy, double &dz)
|
|||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
minimum image convention in periodic dimensions
|
||||
use 1/2 of box size as test
|
||||
for triclinic, also add/subtract tilt factors in other dims as needed
|
||||
changed "if" to "while" to enable distance to
|
||||
far-away ghost atom returned by atom->map() to be wrapped back into box
|
||||
could be problem for looking up atom IDs when cutoff > boxsize
|
||||
this should not be used if atom has moved infinitely far outside box
|
||||
b/c while could iterate forever
|
||||
e.g. fix shake prediction of new position with highly overlapped atoms
|
||||
use minimum_image_once() instead
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Domain::minimum_image(double *delta)
|
||||
{
|
||||
if (triclinic == 0) {
|
||||
if (xperiodic) {
|
||||
while (fabs(delta[0]) > xprd_half) {
|
||||
if (delta[0] < 0.0) delta[0] += xprd;
|
||||
else delta[0] -= xprd;
|
||||
}
|
||||
}
|
||||
if (yperiodic) {
|
||||
while (fabs(delta[1]) > yprd_half) {
|
||||
if (delta[1] < 0.0) delta[1] += yprd;
|
||||
else delta[1] -= yprd;
|
||||
}
|
||||
}
|
||||
if (zperiodic) {
|
||||
while (fabs(delta[2]) > zprd_half) {
|
||||
if (delta[2] < 0.0) delta[2] += zprd;
|
||||
else delta[2] -= zprd;
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
if (zperiodic) {
|
||||
while (fabs(delta[2]) > zprd_half) {
|
||||
if (delta[2] < 0.0) {
|
||||
delta[2] += zprd;
|
||||
delta[1] += yz;
|
||||
delta[0] += xz;
|
||||
} else {
|
||||
delta[2] -= zprd;
|
||||
delta[1] -= yz;
|
||||
delta[0] -= xz;
|
||||
}
|
||||
}
|
||||
}
|
||||
if (yperiodic) {
|
||||
while (fabs(delta[1]) > yprd_half) {
|
||||
if (delta[1] < 0.0) {
|
||||
delta[1] += yprd;
|
||||
delta[0] += xy;
|
||||
} else {
|
||||
delta[1] -= yprd;
|
||||
delta[0] -= xy;
|
||||
}
|
||||
}
|
||||
}
|
||||
if (xperiodic) {
|
||||
while (fabs(delta[0]) > xprd_half) {
|
||||
if (delta[0] < 0.0) delta[0] += xprd;
|
||||
else delta[0] -= xprd;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
minimum image convention in periodic dimensions
|
||||
use 1/2 of box size as test
|
||||
|
|
@ -1929,26 +1870,6 @@ void Domain::set_boundary(int narg, char **arg, int flag)
|
|||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set domain attributes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Domain::set_box(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1) utils::missing_cmd_args(FLERR, "box", error);
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"tilt") == 0) {
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "box tilt", error);
|
||||
if (strcmp(arg[iarg+1],"small") == 0) tiltsmall = 1;
|
||||
else if (strcmp(arg[iarg+1],"large") == 0) tiltsmall = 0;
|
||||
else error->all(FLERR,"Unknown box tilt argument: {}", arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Unknown box keyword: {}", arg[iarg]);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
print box info, orthogonal or triclinic
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -41,7 +41,6 @@ class Domain : protected Pointers {
|
|||
// 3 = shrink-wrap non-per w/ min
|
||||
|
||||
int triclinic; // 0 = orthog box, 1 = triclinic
|
||||
int tiltsmall; // 1 if limit tilt, else 0
|
||||
|
||||
// orthogonal box
|
||||
|
||||
|
|
@ -120,7 +119,7 @@ class Domain : protected Pointers {
|
|||
void box_too_small_check();
|
||||
void subbox_too_small_check(double);
|
||||
void minimum_image(double &, double &, double &);
|
||||
void minimum_image(double *);
|
||||
void minimum_image(double *delta) { minimum_image(delta[0], delta[1], delta[2]); }
|
||||
void minimum_image_once(double *);
|
||||
int closest_image(int, int);
|
||||
int closest_image(const double *const, int);
|
||||
|
|
@ -141,7 +140,6 @@ class Domain : protected Pointers {
|
|||
const std::vector<Region *> get_region_by_style(const std::string &) const;
|
||||
const std::vector<Region *> get_region_list();
|
||||
void set_boundary(int, char **, int);
|
||||
void set_box(int, char **);
|
||||
void print_box(const std::string &);
|
||||
void boundary_string(char *);
|
||||
|
||||
|
|
|
|||
|
|
@ -122,7 +122,7 @@ void Error::universe_one(const std::string &file, int line, const std::string &s
|
|||
void Error::universe_warn(const std::string &file, int line, const std::string &str)
|
||||
{
|
||||
++numwarn;
|
||||
if ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0)) return;
|
||||
if ((maxwarn != 0) && ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0))) return;
|
||||
if (universe->uscreen)
|
||||
fmt::print(universe->uscreen,"WARNING on proc {}: {} ({}:{})\n",
|
||||
universe->me,str,truncpath(file),line);
|
||||
|
|
@ -254,7 +254,7 @@ void Error::_one(const std::string &file, int line, fmt::string_view format,
|
|||
void Error::warning(const std::string &file, int line, const std::string &str)
|
||||
{
|
||||
++numwarn;
|
||||
if ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0)) return;
|
||||
if ((maxwarn != 0) && ((numwarn > maxwarn) || (allwarn > maxwarn) || (maxwarn < 0))) return;
|
||||
std::string mesg = fmt::format("WARNING: {} ({}:{})\n",
|
||||
str,truncpath(file),line);
|
||||
if (screen) fputs(mesg.c_str(),screen);
|
||||
|
|
|
|||
|
|
@ -275,6 +275,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
|
|||
|
||||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf, '\n');
|
||||
if (!next) error->all(FLERR, "Unexpected end of file while reading data section");
|
||||
*next = '\0';
|
||||
|
||||
try {
|
||||
|
|
@ -324,12 +325,12 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
|
|||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return # of lines in section of data file labeled by keyword
|
||||
return # of lines in section of data file labeled by keyword. -1 signals use # of added atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/)
|
||||
{
|
||||
return atom->natoms;
|
||||
return -1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -773,7 +773,6 @@ int Input::execute_command()
|
|||
else if (mycmd == "bond_style") bond_style();
|
||||
else if (mycmd == "bond_write") bond_write();
|
||||
else if (mycmd == "boundary") boundary();
|
||||
else if (mycmd == "box") box();
|
||||
else if (mycmd == "comm_modify") comm_modify();
|
||||
else if (mycmd == "comm_style") comm_style();
|
||||
else if (mycmd == "compute") compute();
|
||||
|
|
@ -1417,15 +1416,6 @@ void Input::boundary()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Input::box()
|
||||
{
|
||||
if (domain->box_exist)
|
||||
error->all(FLERR,"Box command after simulation box is defined");
|
||||
domain->set_box(narg,arg);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Input::comm_modify()
|
||||
{
|
||||
comm->modify_params(narg,arg);
|
||||
|
|
|
|||
|
|
@ -96,7 +96,6 @@ class Input : protected Pointers {
|
|||
void bond_style();
|
||||
void bond_write();
|
||||
void boundary();
|
||||
void box();
|
||||
void comm_modify();
|
||||
void comm_style();
|
||||
void compute();
|
||||
|
|
|
|||
|
|
@ -983,7 +983,7 @@ be called without a valid LAMMPS object handle (it is ignored).
|
|||
**Image masks**
|
||||
|
||||
These settings are related to how LAMMPS stores and interprets periodic images. The values are used
|
||||
internally by the Fortran interface and are not likely to be useful to users.
|
||||
internally by the :doc:`Fortran interface <Fortran>` and are not likely to be useful to users.
|
||||
|
||||
.. list-table::
|
||||
:header-rows: 1
|
||||
|
|
@ -1015,8 +1015,17 @@ internally by the Fortran interface and are not likely to be useful to users.
|
|||
* - box_exist
|
||||
- 1 if the simulation box is defined, 0 if not.
|
||||
See :doc:`create_box`.
|
||||
* - kokkos_active
|
||||
- 1 if the KOKKOS package is compiled in **and** activated, 0 if not.
|
||||
See :doc:`Speed_kokkos`.
|
||||
* - kokkos_nthreads
|
||||
- Number of Kokkos threads per MPI process, 0 if Kokkos is not active.
|
||||
See :doc:`Speed_kokkos`.
|
||||
* - kokkos_ngpus
|
||||
- Number of Kokkos gpus per physical node, 0 if Kokkos is not active or no GPU support.
|
||||
See :doc:`Speed_kokkos`.
|
||||
* - nthreads
|
||||
- Number of requested OpenMP threads for LAMMPS' execution
|
||||
- Number of requested OpenMP threads per MPI process for LAMMPS' execution
|
||||
* - newton_bond
|
||||
- 1 if Newton's 3rd law is applied to bonded interactions, 0 if not.
|
||||
* - newton_pair
|
||||
|
|
@ -1126,6 +1135,9 @@ int lammps_extract_setting(void *handle, const char *keyword)
|
|||
|
||||
if (strcmp(keyword,"dimension") == 0) return lmp->domain->dimension;
|
||||
if (strcmp(keyword,"box_exist") == 0) return lmp->domain->box_exist;
|
||||
if (strcmp(keyword,"kokkos_active") == 0) return (lmp->kokkos) ? 1 : 0;
|
||||
if (strcmp(keyword,"kokkos_nthreads") == 0) return (lmp->kokkos) ? lmp->kokkos->nthreads : 0;
|
||||
if (strcmp(keyword,"kokkos_ngpus") == 0) return (lmp->kokkos) ? lmp->kokkos->ngpus : 0;
|
||||
if (strcmp(keyword,"newton_bond") == 0) return lmp->force->newton_bond;
|
||||
if (strcmp(keyword,"newton_pair") == 0) return lmp->force->newton_pair;
|
||||
if (strcmp(keyword,"triclinic") == 0) return lmp->domain->triclinic;
|
||||
|
|
|
|||
|
|
@ -875,10 +875,13 @@ void ReadData::command(int narg, char **arg)
|
|||
int i;
|
||||
for (i = 0; i < nfix; i++)
|
||||
if (strcmp(keyword, fix_section[i]) == 0) {
|
||||
if (firstpass)
|
||||
if (firstpass) {
|
||||
fix(fix_index[i], keyword);
|
||||
else
|
||||
skip_lines(fix_index[i]->read_data_skip_lines(keyword));
|
||||
} else {
|
||||
auto nskip = fix_index[i]->read_data_skip_lines(keyword);
|
||||
if (nskip < 0) nskip = natoms;
|
||||
skip_lines(nskip);
|
||||
}
|
||||
break;
|
||||
}
|
||||
if (i == nfix)
|
||||
|
|
@ -2225,6 +2228,7 @@ void ReadData::fix(Fix *ifix, char *keyword)
|
|||
int nchunk, eof;
|
||||
|
||||
bigint nline = ifix->read_data_skip_lines(keyword);
|
||||
if (nline < 0) nline = natoms;
|
||||
|
||||
bigint nread = 0;
|
||||
while (nread < nline) {
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ patterns:
|
|||
"""
|
||||
|
||||
def check_pending_tag(f):
|
||||
pattern = re.compile(r'^ *\.\. +version(changed|added):: +TBD')
|
||||
pattern = re.compile(r'^ *\.\. +(version(changed|added)|deprecated):: +TBD')
|
||||
last_line = "\n"
|
||||
lineno = 1
|
||||
errors = set()
|
||||
|
|
|
|||
|
|
@ -209,6 +209,10 @@ TEST_F(LibraryProperties, setting)
|
|||
lammps_command(lmp, "dimension 3");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_active"), 0);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_nthreads"), 0);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_ngpus"), 0);
|
||||
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "world_size"), 1);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "world_rank"), 0);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "universe_size"), 1);
|
||||
|
|
@ -545,3 +549,27 @@ TEST_F(AtomProperties, position)
|
|||
EXPECT_DOUBLE_EQ(x[1][1], 0.1);
|
||||
EXPECT_DOUBLE_EQ(x[1][2], 0.1);
|
||||
}
|
||||
|
||||
TEST(SystemSettings, kokkos)
|
||||
{
|
||||
if (!lammps_config_has_package("KOKKOS")) GTEST_SKIP();
|
||||
if (!lammps_config_accelerator("KOKKOS", "api", "openmp")) GTEST_SKIP();
|
||||
|
||||
// clang-format off
|
||||
const char *args[] = {"SystemSettings", "-log", "none", "-echo", "screen", "-nocite",
|
||||
"-k", "on", "t", "4", "-sf", "kk"};
|
||||
// clang-format on
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args) / sizeof(char *);
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
void *lmp = lammps_open_no_mpi(argc, argv, nullptr);
|
||||
std::string output = ::testing::internal::GetCapturedStdout();
|
||||
if (verbose) std::cout << output;
|
||||
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
||||
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_active"), 1);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_nthreads"), 4);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "kokkos_ngpus"), 0);
|
||||
lammps_close(lmp);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:50 2022
|
||||
lammps_version: 3 Nov 2022
|
||||
tags: generated
|
||||
date_generated: Mon Nov 21 21:52:14 2022
|
||||
epsilon: 1e-12
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
|
|
@ -19,70 +20,70 @@ bond_coeff: ! |
|
|||
equilibrium: 5 1.45 1.37 1.61 2.45 2.85
|
||||
extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 194.9780382216324
|
||||
init_stress: ! |-
|
||||
-2.4024989684355553e+01 -3.8521513996632500e+01 -1.0851224048428129e+01 1.2562604359180053e+01 1.3677283516797356e+01 4.3206731051245653e+00
|
||||
init_energy: 4638.6541482649545
|
||||
init_stress: ! |2-
|
||||
1.8359565872923367e+03 1.1685750963854580e+03 2.2772768476286187e+03 9.0129794950892881e+02 4.5431504423505157e+02 5.8087298633263757e+01
|
||||
init_forces: ! |2
|
||||
1 -1.7791337913398690e+00 -5.2745532425491986e+00 -1.9333096530222391e+00
|
||||
2 7.8999913149794128e-293 6.5010830500033665e-293 -9.2980646648301405e-293
|
||||
1 -2.6166538657523114e+02 -2.1914087860149658e+02 3.0394540432772982e+02
|
||||
2 2.5988625278389128e+02 2.1386632535894739e+02 -3.0587871398075208e+02
|
||||
3 2.4197086198752562e+01 -1.2911571268065043e+01 -1.2153319969868038e+01
|
||||
4 -3.5002110421521651e+00 9.8124800657318079e-01 -2.4834895420880554e+00
|
||||
5 -8.7934593181833831e-01 -1.3513167937313169e+00 4.4900533574430685e+00
|
||||
6 -1.9224405194016612e+01 1.9525383982308810e+01 1.1251608936919853e+01
|
||||
7 2.6580140740726381e-131 -1.3633763941647238e-130 -6.8018769495047054e-130
|
||||
8 1.4462104594211977e+00 -1.2568711136582216e+00 7.3991622652588918e-01
|
||||
9 1.2099652614352605e-300 1.3032068217192395e-300 5.3545155818429412e-300
|
||||
6 -3.1076039081690663e+01 8.0316024755627467e+01 3.1453576435533836e+02
|
||||
7 1.1851633887674051e+01 -6.0790640773318657e+01 -3.0328415541841849e+02
|
||||
8 -9.7268051920198786e+01 -1.0757818812527627e+02 -4.3610490313202450e+02
|
||||
9 9.8714262379619981e+01 1.0632131701161805e+02 4.3684481935855041e+02
|
||||
10 1.8282673669124623e+01 -6.7893037436650294e-01 1.0475143579619905e+01
|
||||
11 -9.5181855408160265e-01 -2.3577388099405021e+00 -3.8685744266264179e+00
|
||||
12 -1.1761121482537199e+01 -1.1840691118605761e+01 8.9587696830512531e+00
|
||||
13 3.9348879648968196e+00 -1.5566010373601853e+00 -7.3956496855403397e-02
|
||||
14 -1.5580348688551586e+00 3.1703943744370217e-01 -4.0404862787928506e+00
|
||||
15 -1.0483110905921594e-01 4.0280962447539723e+00 1.4354708657826634e+00
|
||||
16 -8.1019563183350432e+00 1.2376506087197068e+01 -1.2797826282089627e+01
|
||||
17 -9.6845722000297944e-125 6.7536031200741501e-125 2.5693469616608658e-124
|
||||
18 5.0042083741224387e-291 3.2014176819490257e-291 6.0624670892900674e-291
|
||||
19 -5.0042167517970120e-291 -3.2014265949545701e-291 -6.0624614384187022e-291
|
||||
20 8.3776745733654894e-297 8.9130055442585484e-297 -5.6508713648842736e-297
|
||||
21 5.0373663727594610e-296 1.1676684296048456e-296 8.1823232295641435e-296
|
||||
22 -5.1857245273845906e-296 -1.2567112623130275e-296 -8.1358238807042024e-296
|
||||
23 1.4835815462512912e-297 8.9042832708182009e-298 -4.6499348859940937e-298
|
||||
24 6.5124799547612842e-295 -1.0579059065054233e-295 5.4786730014873485e-295
|
||||
25 -6.5176382072810523e-295 1.0492453069148130e-295 -5.4792561056911984e-295
|
||||
26 5.1582525197680877e-298 8.6605995906103569e-298 5.8310420384964103e-299
|
||||
27 -1.5677247388593395e-295 -1.8232011058192963e-295 -3.8038051984576450e-296
|
||||
28 -3.2483754529644398e-299 1.3960035208884715e-299 -2.1978823514938368e-299
|
||||
29 1.5680495764046360e-295 1.8230615054672073e-295 3.8060030808091389e-296
|
||||
run_energy: 194.9688901668597
|
||||
run_stress: ! |-
|
||||
-2.4084235648269384e+01 -3.8596877573973650e+01 -1.0971337511117875e+01 1.2627485208541385e+01 1.3589007837800324e+01 4.4518443361436777e+00
|
||||
16 9.5774980977037984e+01 -6.0062791522626100e+01 -2.8838655412045694e+02
|
||||
17 -1.0387693729537303e+02 7.2439297609823171e+01 2.7558872783836733e+02
|
||||
18 -1.7290589161548496e+01 -1.3179016873564919e+02 5.1586854877010114e+02
|
||||
19 -2.6734331696703003e+02 -1.7103176128697325e+02 -3.2387856688053216e+02
|
||||
20 2.8463390612857853e+02 3.0282193002262244e+02 -1.9198998188956895e+02
|
||||
21 -1.3595471277589198e+02 -1.6879175531311859e+02 5.0125731248385966e+02
|
||||
22 -2.4366036541914886e+02 -5.9048783595141884e+01 -3.8227595956741493e+02
|
||||
23 3.7961507819504084e+02 2.2784053890826047e+02 -1.1898135291644472e+02
|
||||
24 1.1246873070738241e+02 -4.4920523111996721e+02 2.6503426336875481e+02
|
||||
25 -3.4676635177604459e+02 5.5824357785083230e+01 -2.9151996318153743e+02
|
||||
26 2.3429762106866218e+02 3.9338087333488397e+02 2.6485699812782624e+01
|
||||
27 6.4413473322621542e+01 -4.9624245043025996e+02 1.7125457908457409e+02
|
||||
28 -3.5866433728099020e+02 1.5413756350253817e+02 -2.4267577083822729e+02
|
||||
29 2.9425086395836865e+02 3.4210488692772179e+02 7.1421191753653204e+01
|
||||
run_energy: 4618.705952125554
|
||||
run_stress: ! |2-
|
||||
1.8397902589595653e+03 1.1724487863122602e+03 2.2782759319716897e+03 9.0366417527896033e+02 4.5574598799336053e+02 5.9672689485998390e+01
|
||||
run_forces: ! |2
|
||||
1 -1.7800915383536471e+00 -5.2662174638478936e+00 -1.9311810441446928e+00
|
||||
2 9.1200716389742962e-293 7.5205784896271243e-293 -1.0695855329374170e-292
|
||||
3 2.4188774318819682e+01 -1.2910730800434983e+01 -1.2139174094227805e+01
|
||||
4 -3.4905807721708837e+00 9.7423802985974728e-01 -2.4827066691937869e+00
|
||||
5 -8.7826414385513407e-01 -1.3507945719900971e+00 4.4847167409249762e+00
|
||||
6 -1.9198711248640532e+01 1.9501343007070176e+01 1.1259539605043198e+01
|
||||
7 4.0781500460380220e-131 -2.0934766207882755e-130 -1.0411772151605081e-129
|
||||
8 1.4035232720380466e+00 -1.2181526258990241e+00 7.2552718656771575e-01
|
||||
9 1.4877356608185432e-300 1.5947265521745610e-300 6.5759628249586203e-300
|
||||
10 1.8340705485218969e+01 -7.9602516938863732e-01 1.0533434146468263e+01
|
||||
11 -9.4713695434855716e-01 -2.3455928036230933e+00 -3.8477133980837270e+00
|
||||
12 -1.1753841378581289e+01 -1.1839528950721563e+01 8.9356024501072664e+00
|
||||
13 3.9289793641831325e+00 -1.5460483921060724e+00 -7.3078087497547045e-02
|
||||
14 -1.5515717239320088e+00 3.1019421574866657e-01 -4.0233193667488729e+00
|
||||
15 -1.1312732638809736e-01 4.0290637402465492e+00 1.4439547691915919e+00
|
||||
16 -8.1486573539896803e+00 1.2458251785086224e+01 -1.2885602238406578e+01
|
||||
17 -8.5522515805489358e-125 5.9749160301406998e-125 2.2702237597406565e-124
|
||||
18 2.5382954259673697e-291 1.6282298856292719e-291 3.0672317979786876e-291
|
||||
19 -2.5383561239391082e-291 -1.6282944740463789e-291 -3.0671910793881731e-291
|
||||
20 6.0697971738423079e-296 6.4588417107197222e-296 -4.0718590514496707e-296
|
||||
21 3.1636825215784415e-296 7.4502521705718285e-297 5.0914419661316058e-296
|
||||
22 -3.2413538119513539e-296 -7.9143971383319095e-297 -5.0672219270657353e-296
|
||||
23 7.7671290372912634e-298 4.6414496776008138e-298 -2.4220039065870281e-298
|
||||
24 1.1528889554480086e-295 -1.8584672369333140e-296 9.7061626349018667e-296
|
||||
25 -1.1544439355951613e-295 1.8323577266329387e-296 -9.7079719071127095e-296
|
||||
26 1.5549801471527681e-298 2.6109510300375245e-298 1.8092722108425850e-299
|
||||
27 -1.0502291554946705e-295 -1.2226612584790533e-295 -2.5738911540368265e-296
|
||||
28 -1.8342692926757559e-299 7.8715078988712594e-300 -1.2385711775450889e-299
|
||||
29 1.0504125824239381e-295 1.2225825434000646e-295 2.5751297252143716e-296
|
||||
1 -2.6123247146110606e+02 -2.1919307263372883e+02 3.0237555508171170e+02
|
||||
2 2.5946481985769248e+02 2.1395800468042034e+02 -3.0429922592566089e+02
|
||||
3 2.4104808395110172e+01 -1.2865854073142392e+01 -1.2083882913387207e+01
|
||||
4 -3.4905809559903060e+00 9.7423804418107429e-01 -2.4827069981835161e+00
|
||||
5 -8.7826407777385485e-01 -1.3507948021059526e+00 4.4847171151687837e+00
|
||||
6 -3.1019740486745086e+01 8.0315470917380424e+01 3.1385270827879697e+02
|
||||
7 1.1855512952124167e+01 -6.0859047439602143e+01 -3.0267942216207678e+02
|
||||
8 -9.7139239668224732e+01 -1.0689115264867354e+02 -4.3492337910287688e+02
|
||||
9 9.8566534070284817e+01 1.0565669621976006e+02 4.3567718006870649e+02
|
||||
10 1.8332862345492853e+01 -7.7546447474524260e-01 1.0479498854248916e+01
|
||||
11 -9.4713700870724160e-01 -2.3455930111707550e+00 -3.8477135785159731e+00
|
||||
12 -1.1753839309353248e+01 -1.1839526860590677e+01 8.9356008317611710e+00
|
||||
13 3.9289793641852362e+00 -1.5460483921084245e+00 -7.3078087496756511e-02
|
||||
14 -1.5515717239340792e+00 3.1019421574772799e-01 -4.0233193667504690e+00
|
||||
15 -1.1312732638930625e-01 4.0290637402491614e+00 1.4439547691937924e+00
|
||||
16 9.5584985328403420e+01 -6.0034377008082046e+01 -2.8814471939578698e+02
|
||||
17 -1.0371253029506924e+02 7.2457263526211193e+01 2.7530823253114755e+02
|
||||
18 -1.6734173006461219e+01 -1.3081888486925550e+02 5.1373496074962804e+02
|
||||
19 -2.6689091522155491e+02 -1.7109178558868115e+02 -3.2299073527643651e+02
|
||||
20 2.8362508822801612e+02 3.0191067045793665e+02 -1.9074422547319156e+02
|
||||
21 -1.3584009311603779e+02 -1.6741847021957338e+02 4.9993505971275158e+02
|
||||
22 -2.4342958636297089e+02 -5.9309435913166546e+01 -3.8123078015208006e+02
|
||||
23 3.7926967947900869e+02 2.2672790613273992e+02 -1.1870427956067151e+02
|
||||
24 1.1263526323552287e+02 -4.4826736307529882e+02 2.6440276469069875e+02
|
||||
25 -3.4626849198042515e+02 5.5368312528579615e+01 -2.9134479497708327e+02
|
||||
26 2.3363322874490228e+02 3.9289905054671920e+02 2.6942030286384533e+01
|
||||
27 6.4905554146281361e+01 -4.9580198077236491e+02 1.7016719858461872e+02
|
||||
28 -3.5803172302507875e+02 1.5409360889763499e+02 -2.4188045098816568e+02
|
||||
29 2.9312616887879739e+02 3.4170837187472995e+02 7.1713252403546960e+01
|
||||
...
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:35 2022
|
||||
epsilon: 5e-13
|
||||
lammps_version: 3 Nov 2022
|
||||
date_generated: Wed Nov 23 12:21:08 2022
|
||||
epsilon: 2e-12
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
|
|
@ -33,72 +33,72 @@ extract: ! |
|
|||
nn 2
|
||||
mm 2
|
||||
natoms: 29
|
||||
init_vdwl: 184.28678589160327
|
||||
init_coul: -135.3222017722983
|
||||
init_vdwl: 184.287044185624
|
||||
init_coul: -137.87932620011787
|
||||
init_stress: ! |2-
|
||||
5.1099535412443879e+02 4.9267015856417487e+02 1.0972826650625757e+03 -1.9179119371088936e+02 -3.5985836516943652e+00 1.6890666491875683e+02
|
||||
5.0652399415102809e+02 4.9736621002026737e+02 1.0945023745733126e+03 -1.9301832865224381e+02 1.8762224642096914e-01 1.7162238049862481e+02
|
||||
init_forces: ! |2
|
||||
1 -3.3237622364758597e+00 6.7713954997753760e+01 8.3067188829067177e+01
|
||||
2 3.9621008700560012e+01 3.0171229889604540e+01 -4.8145332639882334e+01
|
||||
3 -3.5364644744971940e+01 -9.6539501255026011e+01 -3.5029548782863188e+01
|
||||
4 -5.3015461109817663e-01 1.6289587757514515e-01 -7.2423374326431356e-01
|
||||
5 -5.9482314827521177e-01 3.6012564229132904e-01 7.9763541784878933e-01
|
||||
6 -2.0517469128198312e+02 2.3641073678086124e+02 2.8403110395134235e+02
|
||||
7 1.4287738299209584e+01 -8.3042673557006708e+01 -4.2404138177988466e+02
|
||||
8 3.4432579872496632e+01 -2.3062478463316680e+01 1.0196257581358861e+02
|
||||
9 2.1504316475975024e+01 1.5520947058320779e+01 8.8721284584619994e+01
|
||||
10 1.3156277736186865e+02 -1.5256269193303697e+02 -4.7528776206099316e+01
|
||||
11 -1.1549608580120421e+00 7.0751627315313514e-01 -1.2306532477500820e+00
|
||||
12 8.2305373454600836e+00 2.8332067643232048e+00 -1.6285990412442382e+00
|
||||
13 2.2152653863898988e-01 -2.5442239617884921e-01 -1.7821156240885982e-02
|
||||
14 -1.4864243248803288e+00 4.9691633196181018e-01 -6.5591950906426355e-01
|
||||
15 1.9536455977505707e-01 4.6553673584615141e-01 -7.3823010387388632e-01
|
||||
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|
||||
17 -1.1530269288646562e+02 8.4705249217102178e+01 2.9252691476710731e+02
|
||||
18 1.2607896146319246e+00 6.6515350853351460e+00 -9.8941034529134715e+00
|
||||
19 1.6182226631729169e+00 -1.6594283813607693e+00 5.6553541079235838e+00
|
||||
20 -3.4521573063242741e+00 -3.1789176785999720e+00 4.2591620921699045e+00
|
||||
21 -1.5230523428245663e+01 -1.8827777303529409e+01 4.5543598985413915e+01
|
||||
22 -2.5331360436022880e+01 -5.4301878248720961e+00 -3.5349975516643234e+01
|
||||
23 4.0112972843495513e+01 2.2949867135700025e+01 -9.6970781334064569e+00
|
||||
1 -3.5396501309981954e+00 6.6944364611585584e+01 8.3059219120660856e+01
|
||||
2 3.9621008700560019e+01 3.0171229889604543e+01 -4.8145332639882334e+01
|
||||
3 -3.5309288471259912e+01 -9.6592073986045776e+01 -3.5059191984527324e+01
|
||||
4 -5.3015461109817674e-01 1.6289587757514493e-01 -7.2423374326431356e-01
|
||||
5 -5.9482314827521177e-01 3.6012564229132926e-01 7.9763541784878955e-01
|
||||
6 -2.0517469128198312e+02 2.3641073678086121e+02 2.8403110395134229e+02
|
||||
7 1.4287738299209584e+01 -8.3042673557006694e+01 -4.2404138177988466e+02
|
||||
8 3.4432579872496632e+01 -2.3062478463316697e+01 1.0196257581358860e+02
|
||||
9 2.1504316475975028e+01 1.5520947058320786e+01 8.8721284584619994e+01
|
||||
10 1.3157989652366749e+02 -1.5248002606214345e+02 -4.7534699865938585e+01
|
||||
11 -1.1549608580120423e+00 7.0751627315313514e-01 -1.2306532477500822e+00
|
||||
12 7.2669942071383717e+00 2.0827730884953919e+00 -9.0483043978096866e-01
|
||||
13 2.2152653863898994e-01 -2.5442239617884937e-01 -1.7821156240885788e-02
|
||||
14 -1.4864243248803288e+00 4.9691633196180973e-01 -6.5591950906426388e-01
|
||||
15 1.9536455977505737e-01 4.6553673584615107e-01 -7.3823010387388610e-01
|
||||
16 1.1427944925864990e+02 -8.2676440560459525e+01 -2.9356712075009648e+02
|
||||
17 -1.1530269288646562e+02 8.4705249217102164e+01 2.9252691476710731e+02
|
||||
18 1.2607896146319251e+00 6.6515350853351460e+00 -9.8941034529134697e+00
|
||||
19 1.6182226631729160e+00 -1.6594283813607693e+00 5.6553541079235821e+00
|
||||
20 -3.4521573063242741e+00 -3.1789176785999724e+00 4.2591620921699054e+00
|
||||
21 -1.5285879701957692e+01 -1.8775204572509647e+01 4.5573242187078066e+01
|
||||
22 -2.5331360436022880e+01 -5.4301878248720943e+00 -3.5349975516643234e+01
|
||||
23 4.0112972843495520e+01 2.2949867135700025e+01 -9.6970781334064569e+00
|
||||
24 6.6473466694181287e+00 -4.2720688813774373e+01 2.5475101119120744e+01
|
||||
25 -3.3278855135511762e+01 2.8247579501663811e+00 -2.7042493390233950e+01
|
||||
26 2.5709355480930235e+01 3.9014887914531776e+01 2.6900053403817590e+00
|
||||
27 1.0035511306793698e+01 -4.5249946085110551e+01 1.8136503701331897e+01
|
||||
28 -3.9953070294941519e+01 1.3962092508592026e+01 -2.6231057257176037e+01
|
||||
29 3.0657392434855581e+01 3.0940622604427993e+01 8.6697893689665211e+00
|
||||
run_vdwl: 182.40565476045293
|
||||
run_coul: -135.3428229317011
|
||||
27 1.0999054445115412e+01 -4.4499512409282737e+01 1.7412735099868630e+01
|
||||
28 -3.9953070294941519e+01 1.3962092508592027e+01 -2.6231057257176040e+01
|
||||
29 3.0657392434855577e+01 3.0940622604427993e+01 8.6697893689665193e+00
|
||||
run_vdwl: 182.40627457531505
|
||||
run_coul: -137.89878255208336
|
||||
run_stress: ! |2-
|
||||
5.0949331883645084e+02 4.9079274612266465e+02 1.0779924919705209e+03 -1.8978874005409725e+02 -2.3414288930535676e+00 1.6680086396779814e+02
|
||||
5.0502284487804911e+02 4.9549254038893065e+02 1.0752131218453601e+03 -1.9101402318764428e+02 1.4448370451390913e+00 1.6951693900962570e+02
|
||||
run_forces: ! |2
|
||||
1 -3.0222512967714557e+00 6.7548505252631742e+01 8.2368596588550062e+01
|
||||
2 3.9249247328631569e+01 2.9923489231546629e+01 -4.7570871930892892e+01
|
||||
3 -3.5327226055520775e+01 -9.6102750283993871e+01 -3.4890589040756382e+01
|
||||
4 -5.2696455605069259e-01 1.6213860296922811e-01 -7.2430457126338410e-01
|
||||
5 -5.9400169113171586e-01 3.6136912208033589e-01 7.9530286564994024e-01
|
||||
6 -2.0274433560773628e+02 2.3284786713406370e+02 2.7401951211582013e+02
|
||||
7 1.4053553144930220e+01 -8.1102084254822103e+01 -4.1219124551744085e+02
|
||||
8 3.2718675446198795e+01 -2.1551046804011083e+01 1.0097962112112319e+02
|
||||
9 2.1323856224128093e+01 1.5222193966786529e+01 8.7834851199368813e+01
|
||||
10 1.3130268818222987e+02 -1.5219622702094762e+02 -4.7515342312770102e+01
|
||||
11 -1.1541261444752642e+00 7.1381752451384339e-01 -1.2230561924848902e+00
|
||||
12 8.2264000446385346e+00 2.8299212831552727e+00 -1.6299507774035358e+00
|
||||
13 2.1792987819368359e-01 -2.5267817510362128e-01 -1.9040070778804069e-02
|
||||
14 -1.4863827602148627e+00 4.9691341825375590e-01 -6.4929126993868946e-01
|
||||
15 1.9516446161304488e-01 4.6409461483290748e-01 -7.4066880359248788e-01
|
||||
16 1.1245063534493042e+02 -8.2380964098503739e+01 -2.8939941367324343e+02
|
||||
17 -1.1367888495468203e+02 8.3736413965239862e+01 2.8833591319216583e+02
|
||||
18 1.2131213413750925e+00 6.6087858905244472e+00 -9.8443684782076062e+00
|
||||
19 1.6546892701962139e+00 -1.6335518483372100e+00 5.6675264381026587e+00
|
||||
20 -3.4406155231052553e+00 -3.1608955862760086e+00 4.2021081664244280e+00
|
||||
21 -1.5380842837515630e+01 -1.8832663749099712e+01 4.5639191584555739e+01
|
||||
22 -2.5437261250740086e+01 -5.4851555768258553e+00 -3.5409747254511750e+01
|
||||
23 4.0368809860056317e+01 2.3008461599616822e+01 -9.7324663526701478e+00
|
||||
24 7.1229399666679027e+00 -4.3444645139181588e+01 2.6085435505612736e+01
|
||||
25 -3.4137823679541398e+01 2.8946896673905611e+00 -2.7774080649897098e+01
|
||||
26 2.6093689208699011e+01 3.9671650206452789e+01 2.8124886686652082e+00
|
||||
27 1.0189565500107717e+01 -4.5358416256293751e+01 1.8141445825723800e+01
|
||||
28 -4.0123206182868742e+01 1.4015089779144132e+01 -2.6301107890805710e+01
|
||||
29 3.0672957337757669e+01 3.0995677534193614e+01 8.7335515148952023e+00
|
||||
1 -3.2370828229989943e+00 6.6780774771428867e+01 8.2360566992843957e+01
|
||||
2 3.9248669659652556e+01 2.9923101710814461e+01 -4.7570156486162247e+01
|
||||
3 -3.5272405495891725e+01 -9.6156898011190052e+01 -3.4920858821878639e+01
|
||||
4 -5.2696307806019427e-01 1.6213782144861011e-01 -7.2430297098202856e-01
|
||||
5 -5.9400132072875222e-01 3.6136881819958322e-01 7.9530174833943768e-01
|
||||
6 -2.0274433109253258e+02 2.3284785750828254e+02 2.7401951291433039e+02
|
||||
7 1.4053553193905296e+01 -8.1102076691627317e+01 -4.1219125509985423e+02
|
||||
8 3.2718449282709940e+01 -2.1550864085726676e+01 1.0097970359571399e+02
|
||||
9 2.1323849598698548e+01 1.5222193680732165e+01 8.7834847272654116e+01
|
||||
10 1.3131984144877813e+02 -1.5211385896116542e+02 -4.7521267129265915e+01
|
||||
11 -1.1541259655305498e+00 7.1381836660091746e-01 -1.2230539280652590e+00
|
||||
12 7.2630852175005964e+00 2.0798061880380749e+00 -9.0633631991268937e-01
|
||||
13 2.1792142656044974e-01 -2.5267485273151963e-01 -1.9040900180560982e-02
|
||||
14 -1.4863809886398240e+00 4.9691277039032383e-01 -6.4928587974626595e-01
|
||||
15 1.9516412586808574e-01 4.6408847437290568e-01 -7.4067142611860370e-01
|
||||
16 1.1264998906650452e+02 -8.1693726909197835e+01 -2.8938652282069330e+02
|
||||
17 -1.1367940494205878e+02 8.3736184613376594e+01 2.8833692617302631e+02
|
||||
18 1.2131256191519586e+00 6.6087841118467869e+00 -9.8443636765781175e+00
|
||||
19 1.6546867296048959e+00 -1.6335521580158148e+00 5.6675246971307507e+00
|
||||
20 -3.4406162815803181e+00 -3.1608941993411719e+00 4.2021061175034422e+00
|
||||
21 -1.5436168448451303e+01 -1.8780058922578032e+01 4.5668818732530838e+01
|
||||
22 -2.5437256643599888e+01 -5.4851610900512116e+00 -3.5409746057405300e+01
|
||||
23 4.0368779518163102e+01 2.3008433743607917e+01 -9.7324579117657564e+00
|
||||
24 7.1229403171558960e+00 -4.3444642379685369e+01 2.6085431366299698e+01
|
||||
25 -3.4137823381351410e+01 2.8946870622451546e+00 -2.7774076485443004e+01
|
||||
26 2.6093689507109417e+01 3.9671649820489279e+01 2.8124906008412616e+00
|
||||
27 1.1152133422843132e+01 -4.4609063038241878e+01 1.7417265391517304e+01
|
||||
28 -4.0123145645809892e+01 1.4014953690801475e+01 -2.6300937504650808e+01
|
||||
29 3.0673827973027787e+01 3.0996718146876649e+01 8.7338378159710270e+00
|
||||
...
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:35 2022
|
||||
lammps_version: 3 Nov 2022
|
||||
date_generated: Wed Nov 23 12:21:08 2022
|
||||
epsilon: 7.5e-13
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
|
|
@ -39,72 +39,72 @@ extract: ! |
|
|||
mm 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 184.28678589160327
|
||||
init_vdwl: 184.287044185624
|
||||
init_coul: 225.82181512692495
|
||||
init_stress: ! |2-
|
||||
5.1535561642229106e+02 5.0058662653359033e+02 1.1159625282020661e+03 -1.8397466102442883e+02 -2.0220636765660638e+00 1.7544854550792292e+02
|
||||
5.1535625659153879e+02 5.0058721227699067e+02 1.1159628277106565e+03 -1.8397448571567824e+02 -2.0224936628921029e+00 1.7544839728662993e+02
|
||||
init_forces: ! |2
|
||||
1 -3.0654526282473653e+00 6.6615864099533127e+01 8.2943973715838268e+01
|
||||
2 3.9068866013811309e+01 2.9455617832505151e+01 -4.7591021495719247e+01
|
||||
3 -3.5280048507313708e+01 -9.6589706921967377e+01 -3.5074530442718626e+01
|
||||
4 -6.6290078829733745e-01 1.7069498108397532e-01 -6.5698974844320646e-01
|
||||
5 -7.3666031116459629e-01 3.1866503947918778e-01 8.0597153193899140e-01
|
||||
6 -2.0569141405030027e+02 2.3627567491105717e+02 2.8443813098936624e+02
|
||||
7 1.4533357696957466e+01 -8.2901362570668283e+01 -4.2411675286042595e+02
|
||||
8 3.4572734326141102e+01 -2.2709011166557751e+01 1.0190201388959704e+02
|
||||
9 2.1302134918689685e+01 1.5382116555420744e+01 8.8486496066808485e+01
|
||||
10 1.3163065394972341e+02 -1.5255187760681488e+02 -4.7566872183542166e+01
|
||||
11 -1.0673114564038046e+00 6.0655281622864732e-01 -1.2545988594461333e+00
|
||||
12 7.7809585200300058e+00 3.1160398793201316e+00 -1.4701791888504216e+00
|
||||
13 5.3014557250212346e-01 -2.5075115207640880e-01 -1.8692015200156273e-01
|
||||
14 -1.3123789187002088e+00 4.0626415990577358e-01 -7.3662740015731798e-01
|
||||
15 3.2883564820812672e-01 4.2874288932750715e-01 -7.8340375997477496e-01
|
||||
16 1.1459556574512777e+02 -8.2820743414973677e+01 -2.9444590351113385e+02
|
||||
17 -1.1537978255115650e+02 8.4825361701504292e+01 2.9365401995966459e+02
|
||||
18 3.5910667886316144e-01 4.7762805533526835e+00 -7.8633657965049659e+00
|
||||
19 1.9899962970618248e+00 -7.2139551998620521e-01 5.5216058955830674e+00
|
||||
20 -2.9130824841870520e+00 -3.9872076040781708e+00 4.1253374345150986e+00
|
||||
21 -1.5875835643064573e+01 -1.5889863208570942e+01 4.7172258432278930e+01
|
||||
22 -2.5015657684773860e+01 -7.0704088600117272e+00 -3.6174324111002065e+01
|
||||
23 4.0477622003880207e+01 2.3373134480751212e+01 -1.0495870801503438e+01
|
||||
1 -3.0654561493791848e+00 6.6615850470254358e+01 8.2943973912197166e+01
|
||||
2 3.9068866013811295e+01 2.9455617832505151e+01 -4.7591021495719239e+01
|
||||
3 -3.5280084914007190e+01 -9.6589672345953218e+01 -3.5074510946988802e+01
|
||||
4 -6.6290078829733778e-01 1.7069498108397516e-01 -6.5698974844320646e-01
|
||||
5 -7.3666031116459629e-01 3.1866503947918762e-01 8.0597153193899174e-01
|
||||
6 -2.0569141405030027e+02 2.3627567491105717e+02 2.8443813098936630e+02
|
||||
7 1.4533357696957466e+01 -8.2901362570668297e+01 -4.2411675286042589e+02
|
||||
8 3.4572734326141102e+01 -2.2709011166557758e+01 1.0190201388959706e+02
|
||||
9 2.1302134918689685e+01 1.5382116555420737e+01 8.8486496066808471e+01
|
||||
10 1.3163065501356638e+02 -1.5255187246967631e+02 -4.7566872551658555e+01
|
||||
11 -1.0673114564038049e+00 6.0655281622864710e-01 -1.2545988594461335e+00
|
||||
12 7.7810444548679740e+00 3.1161068077157283e+00 -1.4702437390869596e+00
|
||||
13 5.3014557250212357e-01 -2.5075115207640869e-01 -1.8692015200156262e-01
|
||||
14 -1.3123789187002091e+00 4.0626415990577341e-01 -7.3662740015731820e-01
|
||||
15 3.2883564820812672e-01 4.2874288932750720e-01 -7.8340375997477496e-01
|
||||
16 1.1459556820241663e+02 -8.2820734922833438e+01 -2.9444590333937629e+02
|
||||
17 -1.1537978255115650e+02 8.4825361701504292e+01 2.9365401995966465e+02
|
||||
18 3.5910667886316239e-01 4.7762805533526844e+00 -7.8633657965049650e+00
|
||||
19 1.9899962970618255e+00 -7.2139551998620499e-01 5.5216058955830682e+00
|
||||
20 -2.9130824841870520e+00 -3.9872076040781712e+00 4.1253374345150977e+00
|
||||
21 -1.5875799236371092e+01 -1.5889897784585100e+01 4.7172238936549107e+01
|
||||
22 -2.5015657684773856e+01 -7.0704088600117272e+00 -3.6174324111002072e+01
|
||||
23 4.0477622003880199e+01 2.3373134480751215e+01 -1.0495870801503438e+01
|
||||
24 7.4996662349142147e+00 -4.3426856761904077e+01 2.2815324534810056e+01
|
||||
25 -3.3807147976811798e+01 2.9988027310973613e+00 -2.7577372367283733e+01
|
||||
26 2.5746888892709649e+01 4.0174454060022633e+01 4.1505216253578832e+00
|
||||
27 1.0861995979992932e+01 -4.6328822142297405e+01 1.8883010243779164e+01
|
||||
28 -4.0470174882584459e+01 1.5020795051869365e+01 -2.6766823901697389e+01
|
||||
29 2.9999319404392626e+01 3.1302945187447804e+01 7.8628922608669090e+00
|
||||
run_vdwl: 182.40255929507265
|
||||
run_coul: 225.80523122237145
|
||||
26 2.5746888892709649e+01 4.0174454060022640e+01 4.1505216253578832e+00
|
||||
27 1.0861910045154971e+01 -4.6328889070692995e+01 1.8883074794015705e+01
|
||||
28 -4.0470174882584466e+01 1.5020795051869364e+01 -2.6766823901697389e+01
|
||||
29 2.9999319404392619e+01 3.1302945187447808e+01 7.8628922608669081e+00
|
||||
run_vdwl: 182.4028175410934
|
||||
run_coul: 225.8052312234039
|
||||
run_stress: ! |2-
|
||||
5.1384631551491782e+02 4.9870417055031982e+02 1.0966342093912015e+03 -1.8197324336578851e+02 -7.7105078556388151e-01 1.7333789878387816e+02
|
||||
5.1384695555524797e+02 4.9870475622702440e+02 1.0966345088415544e+03 -1.8197306815785140e+02 -7.7148065920433828e-01 1.7333775064278868e+02
|
||||
run_forces: ! |2
|
||||
1 -2.7683190788522740e+00 6.6449095933852917e+01 8.2247798763054263e+01
|
||||
2 3.8702194737017720e+01 2.9212212087553127e+01 -4.7019606503568262e+01
|
||||
3 -3.5243454712977965e+01 -9.6154953753202179e+01 -3.4936504547233788e+01
|
||||
4 -6.5977694961123645e-01 1.7011044348999105e-01 -6.5636000725760957e-01
|
||||
5 -7.3566520752177100e-01 3.2004552783623724e-01 8.0428279587216267e-01
|
||||
6 -2.0326269571945986e+02 2.3271299846462981e+02 2.7442711029956843e+02
|
||||
7 1.4300022426556877e+01 -8.0959802783401827e+01 -4.1226588339681336e+02
|
||||
8 3.2858865815794836e+01 -2.1199692716643838e+01 1.0091081448967174e+02
|
||||
9 2.1122712553671928e+01 1.5084944366082448e+01 8.7605507483986727e+01
|
||||
10 1.3136998924075732e+02 -1.5218480626807963e+02 -4.7552578947927799e+01
|
||||
11 -1.0661815519248918e+00 6.1243966630893298e-01 -1.2462619432373649e+00
|
||||
12 7.7760226803888877e+00 3.1127903917502313e+00 -1.4744683960464942e+00
|
||||
13 5.2674567614856260e-01 -2.4917750370694214e-01 -1.8723948852408964e-01
|
||||
14 -1.3120520030459297e+00 4.0614121490067551e-01 -7.2914653810616858e-01
|
||||
15 3.2867638556545775e-01 4.2750422420803547e-01 -7.8475645386864112e-01
|
||||
16 1.1296204426736116e+02 -8.1834725178344044e+01 -2.9024712497341085e+02
|
||||
17 -1.1375160210673371e+02 8.3851461683740141e+01 2.8944627577285223e+02
|
||||
18 3.0738271507674780e-01 4.7275452047652715e+00 -7.8225407640491564e+00
|
||||
19 2.0274564843313856e+00 -6.9333851982762851e-01 5.5367198586609998e+00
|
||||
20 -2.8992094355719793e+00 -3.9662518101373307e+00 4.0716447585419049e+00
|
||||
21 -1.6026802334504676e+01 -1.5883942063853187e+01 4.7256123626066532e+01
|
||||
22 -2.5118526633549543e+01 -7.1302229414472507e+00 -3.6226155173751806e+01
|
||||
23 4.0731190500597606e+01 2.3426593800522156e+01 -1.0527512154067734e+01
|
||||
24 7.9759015134187958e+00 -4.4140032709411031e+01 2.3421942671527756e+01
|
||||
25 -3.4663427794559517e+01 3.0656502790867206e+00 -2.8305771158291158e+01
|
||||
26 2.6127821098995337e+01 4.0822834309889892e+01 4.2748874027969199e+00
|
||||
27 1.1011144648995060e+01 -4.6436392031462617e+01 1.8878782007839565e+01
|
||||
28 -4.0634772085359785e+01 1.5071357955251854e+01 -2.6829753884337045e+01
|
||||
29 3.0014314868995513e+01 3.1359612725649200e+01 7.9297744000519685e+00
|
||||
1 -2.7683225482283809e+00 6.6449082401023148e+01 8.2247798981789643e+01
|
||||
2 3.8702194726711895e+01 2.9212212080708927e+01 -4.7019606490893651e+01
|
||||
3 -3.5243491151797656e+01 -9.6154919282511642e+01 -3.4936485094808461e+01
|
||||
4 -6.5977694998018921e-01 1.7011044357157604e-01 -6.5636000759126256e-01
|
||||
5 -7.3566520753163211e-01 3.2004552769599226e-01 8.0428279621249554e-01
|
||||
6 -2.0326269572309553e+02 2.3271299846832454e+02 2.7442711030170454e+02
|
||||
7 1.4300022426979604e+01 -8.0959802783845490e+01 -4.1226588339625141e+02
|
||||
8 3.2858865805990142e+01 -2.1199692705942155e+01 1.0091081449262803e+02
|
||||
9 2.1122712553325698e+01 1.5084944366414280e+01 8.7605507484381420e+01
|
||||
10 1.3136999033009897e+02 -1.5218480112815018e+02 -4.7552579328976627e+01
|
||||
11 -1.0661815520486129e+00 6.1243966623508861e-01 -1.2462619432216921e+00
|
||||
12 7.7761085744513680e+00 3.1128572757481363e+00 -1.4745329169765931e+00
|
||||
13 5.2674567689395169e-01 -2.4917750397088440e-01 -1.8723948847901425e-01
|
||||
14 -1.3120520033096184e+00 4.0614121494992139e-01 -7.2914653857642009e-01
|
||||
15 3.2867638550341521e-01 4.2750422476572436e-01 -7.8475645363096747e-01
|
||||
16 1.1296204673281163e+02 -8.1834716679121783e+01 -2.9024712481379936e+02
|
||||
17 -1.1375160211353307e+02 8.3851461680840046e+01 2.8944627578500337e+02
|
||||
18 3.0738271486215951e-01 4.7275452050710545e+00 -7.8225407641446587e+00
|
||||
19 2.0274564844173879e+00 -6.9333851990195527e-01 5.5367198587099775e+00
|
||||
20 -2.8992094355377156e+00 -3.9662518102337199e+00 4.0716447585813889e+00
|
||||
21 -1.6026765950606343e+01 -1.5883976653313633e+01 4.7256104141803178e+01
|
||||
22 -2.5118526637643978e+01 -7.1302229387234384e+00 -3.6226155173665845e+01
|
||||
23 4.0731190519921540e+01 2.3426593817372833e+01 -1.0527512159329465e+01
|
||||
24 7.9759015134016398e+00 -4.4140032709414839e+01 2.3421942671485997e+01
|
||||
25 -3.4663427794542088e+01 3.0656502790778966e+00 -2.8305771158233721e+01
|
||||
26 2.6127821099004976e+01 4.0822834309892897e+01 4.2748874028091679e+00
|
||||
27 1.1011058821774000e+01 -4.6436458847462333e+01 1.8878846579362040e+01
|
||||
28 -4.0634772090200137e+01 1.5071357967752173e+01 -2.6829753899915300e+01
|
||||
29 3.0014314791906596e+01 3.1359612633147766e+01 7.9297743740230970e+00
|
||||
...
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:35 2022
|
||||
lammps_version: 3 Nov 2022
|
||||
date_generated: Wed Nov 23 12:21:08 2022
|
||||
epsilon: 5e-12
|
||||
skip_tests: gpu
|
||||
prerequisites: ! |
|
||||
|
|
@ -39,72 +39,72 @@ extract: ! |
|
|||
mm 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 184.28678589160327
|
||||
init_coul: 225.82185134782813
|
||||
init_vdwl: 184.287044185624
|
||||
init_coul: 225.8218513478281
|
||||
init_stress: ! |2-
|
||||
5.1535563668501300e+02 5.0058663228965906e+02 1.1159625416266908e+03 -1.8397465772983549e+02 -2.0220541814186075e+00 1.7544854959858193e+02
|
||||
5.1535627685426095e+02 5.0058721803305957e+02 1.1159628411352805e+03 -1.8397448242108504e+02 -2.0224841677449517e+00 1.7544840137728934e+02
|
||||
init_forces: ! |2
|
||||
1 -3.0654541322175968e+00 6.6615863677171617e+01 8.2943971924222254e+01
|
||||
1 -3.0654576533494127e+00 6.6615850047892891e+01 8.2943972120581122e+01
|
||||
2 3.9068865513677615e+01 2.9455617099928201e+01 -4.7591020157569005e+01
|
||||
3 -3.5280048398649157e+01 -9.6589707037291518e+01 -3.5074530567243464e+01
|
||||
4 -6.6290079171346505e-01 1.7069544377339213e-01 -6.5698955820925042e-01
|
||||
5 -7.3666014335594099e-01 3.1866598696678072e-01 8.0597176706748563e-01
|
||||
6 -2.0569141450616158e+02 2.3627567585415383e+02 2.8443812919367736e+02
|
||||
7 1.4533356899344014e+01 -8.2901362616912394e+01 -4.2411675492205256e+02
|
||||
8 3.4572733596567637e+01 -2.2709011431274082e+01 1.0190201593114163e+02
|
||||
9 2.1302136717273982e+01 1.5382115964517633e+01 8.8486497965632879e+01
|
||||
10 1.3163065406656153e+02 -1.5255187717021275e+02 -4.7566872791707098e+01
|
||||
11 -1.0673115707973471e+00 6.0655351752474329e-01 -1.2545987554013556e+00
|
||||
12 7.7809586887870594e+00 3.1160399372388605e+00 -1.4701800924466619e+00
|
||||
13 5.3014565234400191e-01 -2.5075128500262650e-01 -1.8692002168697544e-01
|
||||
14 -1.3123790631110117e+00 4.0626403937555045e-01 -7.3662725812128549e-01
|
||||
15 3.2883559728278194e-01 4.2874259749687393e-01 -7.8340316469885862e-01
|
||||
16 1.1459556694004317e+02 -8.2820744612264363e+01 -2.9444590318663785e+02
|
||||
17 -1.1537978278388316e+02 8.4825361961770099e+01 2.9365401989722858e+02
|
||||
18 3.5910722977056597e-01 4.7762805084795117e+00 -7.8633666628226111e+00
|
||||
19 1.9899942949153411e+00 -7.2139693846497077e-01 5.5216057638120377e+00
|
||||
20 -2.9130806625761494e+00 -3.9872064081602967e+00 4.1253385233400710e+00
|
||||
21 -1.5875836014985955e+01 -1.5889862643744696e+01 4.7172259002528357e+01
|
||||
22 -2.5015660385936844e+01 -7.0704105161901349e+00 -3.6174325746867012e+01
|
||||
23 4.0477625196492205e+01 2.3373135655738206e+01 -1.0495869916757165e+01
|
||||
3 -3.5280084805342639e+01 -9.6589672461277360e+01 -3.5074511071513633e+01
|
||||
4 -6.6290079171346505e-01 1.7069544377339210e-01 -6.5698955820925031e-01
|
||||
5 -7.3666014335594110e-01 3.1866598696678072e-01 8.0597176706748597e-01
|
||||
6 -2.0569141450616158e+02 2.3627567585415389e+02 2.8443812919367736e+02
|
||||
7 1.4533356899344010e+01 -8.2901362616912380e+01 -4.2411675492205251e+02
|
||||
8 3.4572733596567609e+01 -2.2709011431274096e+01 1.0190201593114163e+02
|
||||
9 2.1302136717273982e+01 1.5382115964517647e+01 8.8486497965632879e+01
|
||||
10 1.3163065513040453e+02 -1.5255187203307418e+02 -4.7566873159823480e+01
|
||||
11 -1.0673115707973471e+00 6.0655351752474307e-01 -1.2545987554013558e+00
|
||||
12 7.7810446236250250e+00 3.1161068656344568e+00 -1.4702446426831981e+00
|
||||
13 5.3014565234400202e-01 -2.5075128500262667e-01 -1.8692002168697544e-01
|
||||
14 -1.3123790631110113e+00 4.0626403937555039e-01 -7.3662725812128527e-01
|
||||
15 3.2883559728278206e-01 4.2874259749687393e-01 -7.8340316469885873e-01
|
||||
16 1.1459556939733203e+02 -8.2820736120124138e+01 -2.9444590301488040e+02
|
||||
17 -1.1537978278388316e+02 8.4825361961770113e+01 2.9365401989722858e+02
|
||||
18 3.5910722977056608e-01 4.7762805084795099e+00 -7.8633666628226058e+00
|
||||
19 1.9899942949153395e+00 -7.2139693846497099e-01 5.5216057638120368e+00
|
||||
20 -2.9130806625761498e+00 -3.9872064081602954e+00 4.1253385233400701e+00
|
||||
21 -1.5875799608292471e+01 -1.5889897219758861e+01 4.7172239506798533e+01
|
||||
22 -2.5015660385936840e+01 -7.0704105161901358e+00 -3.6174325746867005e+01
|
||||
23 4.0477625196492198e+01 2.3373135655738203e+01 -1.0495869916757163e+01
|
||||
24 7.4996665312988062e+00 -4.3426856369883282e+01 2.2815324088130364e+01
|
||||
25 -3.3807149952465473e+01 2.9988014337987989e+00 -2.7577373212676150e+01
|
||||
26 2.5746891183225689e+01 4.0174455514363842e+01 4.1505232593253609e+00
|
||||
27 1.0861995864629581e+01 -4.6328821976580151e+01 1.8883010049856995e+01
|
||||
28 -4.0470177594126923e+01 1.5020794116966732e+01 -2.6766825117758021e+01
|
||||
29 2.9999322027766638e+01 3.1302945696716428e+01 7.8628937666919105e+00
|
||||
run_vdwl: 182.40255928657774
|
||||
run_coul: 225.80526621801556
|
||||
26 2.5746891183225689e+01 4.0174455514363835e+01 4.1505232593253609e+00
|
||||
27 1.0861909929791622e+01 -4.6328888904975756e+01 1.8883074600093536e+01
|
||||
28 -4.0470177594126930e+01 1.5020794116966732e+01 -2.6766825117758025e+01
|
||||
29 2.9999322027766638e+01 3.1302945696716428e+01 7.8628937666919114e+00
|
||||
run_vdwl: 182.40281753260578
|
||||
run_coul: 225.80526621917056
|
||||
run_stress: ! |2-
|
||||
5.1384633450263470e+02 4.9870417152157029e+02 1.0966342229480442e+03 -1.8197323856665997e+02 -7.7104387031605370e-01 1.7333790492919763e+02
|
||||
5.1384697454379841e+02 4.9870475719746798e+02 1.0966345223981718e+03 -1.8197306335846980e+02 -7.7147374345845032e-01 1.7333775678806884e+02
|
||||
run_forces: ! |2
|
||||
1 -2.7683205204507280e+00 6.6449095490165703e+01 8.2247797711895885e+01
|
||||
2 3.8702193821877493e+01 2.9212211419425969e+01 -4.7019604804325617e+01
|
||||
3 -3.5243454585514591e+01 -9.6154953863738911e+01 -3.4936504643788560e+01
|
||||
4 -6.5977687131041252e-01 1.7011085278366439e-01 -6.5635985341126124e-01
|
||||
5 -7.3566505234358270e-01 3.2004653103552905e-01 8.0428307532511589e-01
|
||||
6 -2.0326269614835340e+02 2.3271299913843555e+02 2.7442710822013873e+02
|
||||
7 1.4300021996054623e+01 -8.0959802494991251e+01 -4.1226588541677728e+02
|
||||
8 3.2858865265765651e+01 -2.1199693568720125e+01 1.0091081733429107e+02
|
||||
9 2.1122714604067934e+01 1.5084943250328770e+01 8.7605509332947179e+01
|
||||
10 1.3136998941143941e+02 -1.5218480590048722e+02 -4.7552579577409830e+01
|
||||
11 -1.0661815608329375e+00 6.1244026211185132e-01 -1.2462619124968015e+00
|
||||
12 7.7760233760077231e+00 3.1127902634122728e+00 -1.4744694804987457e+00
|
||||
13 5.2674586924271427e-01 -2.4917758586878880e-01 -1.8723934835850795e-01
|
||||
14 -1.3120523259791150e+00 4.0614108203397964e-01 -7.2914636677516875e-01
|
||||
15 3.2867610981988737e-01 4.2750390948272482e-01 -7.8475586802253572e-01
|
||||
16 1.1296204447867072e+02 -8.1834725270478103e+01 -2.9024712501702589e+02
|
||||
17 -1.1375160235079549e+02 8.3851462518713276e+01 2.8944627514695969e+02
|
||||
18 3.0738345014064944e-01 4.7275451584201162e+00 -7.8225421226147951e+00
|
||||
19 2.0274544872239728e+00 -6.9334025263478072e-01 5.5367196067976767e+00
|
||||
20 -2.8992075327228490e+00 -3.9662506277601803e+00 4.0716458277265861e+00
|
||||
21 -1.6026802838192324e+01 -1.5883941405520059e+01 4.7256124362739875e+01
|
||||
22 -2.5118529350290316e+01 -7.1302246487029537e+00 -3.6226156710291576e+01
|
||||
23 4.0731193744183564e+01 2.3426594982025247e+01 -1.0527511305357223e+01
|
||||
24 7.9759015601633747e+00 -4.4140032390736621e+01 2.3421941942737131e+01
|
||||
25 -3.4663429593566200e+01 3.0656489475373521e+00 -2.8305771699474640e+01
|
||||
26 2.6127823323620827e+01 4.0822835743219649e+01 4.2748889953069069e+00
|
||||
27 1.1011144344413010e+01 -4.6436391929690870e+01 1.8878781879279799e+01
|
||||
28 -4.0634774700271556e+01 1.5071357061734957e+01 -2.6829755168650092e+01
|
||||
29 3.0014317587931910e+01 3.1359613328463354e+01 7.9297758591329561e+00
|
||||
1 -2.7683239898506331e+00 6.6449081957468636e+01 8.2247797930661747e+01
|
||||
2 3.8702193811582511e+01 2.9212211412571293e+01 -4.7019604791653393e+01
|
||||
3 -3.5243491024333295e+01 -9.6154919393054271e+01 -3.4936485191359907e+01
|
||||
4 -6.5977687168190458e-01 1.7011085284653316e-01 -6.5635985375283568e-01
|
||||
5 -7.3566505234995705e-01 3.2004653083828444e-01 8.0428307567331736e-01
|
||||
6 -2.0326269615165228e+02 2.3271299914190627e+02 2.7442710822226110e+02
|
||||
7 1.4300021996095619e+01 -8.0959802495291143e+01 -4.1226588541635073e+02
|
||||
8 3.2858865255384757e+01 -2.1199693557841638e+01 1.0091081733750200e+02
|
||||
9 2.1122714603970017e+01 1.5084943250468159e+01 8.7605509333063679e+01
|
||||
10 1.3136999050087155e+02 -1.5218480076049869e+02 -4.7552579958511345e+01
|
||||
11 -1.0661815608470382e+00 6.1244026210440039e-01 -1.2462619124717631e+00
|
||||
12 7.7761092701979475e+00 3.1128571473156490e+00 -1.4745340012267927e+00
|
||||
13 5.2674586999352180e-01 -2.4917758618970665e-01 -1.8723934833596209e-01
|
||||
14 -1.3120523262243908e+00 4.0614108204631622e-01 -7.2914636724809301e-01
|
||||
15 3.2867610975969386e-01 4.2750391001876636e-01 -7.8475586778582129e-01
|
||||
16 1.1296204694413225e+02 -8.1834716771070589e+01 -2.9024712485782527e+02
|
||||
17 -1.1375160235744099e+02 8.3851462515852432e+01 2.8944627515943881e+02
|
||||
18 3.0738344999939127e-01 4.7275451584991384e+00 -7.8225421226024254e+00
|
||||
19 2.0274544872772347e+00 -6.9334025264774690e-01 5.5367196067971562e+00
|
||||
20 -2.8992075326987843e+00 -3.9662506277824492e+00 4.0716458277284353e+00
|
||||
21 -1.6026766454385204e+01 -1.5883975994889351e+01 4.7256104878610991e+01
|
||||
22 -2.5118529354380893e+01 -7.1302246459886085e+00 -3.6226156710215299e+01
|
||||
23 4.0731193763533284e+01 2.3426594998848003e+01 -1.0527511310640200e+01
|
||||
24 7.9759015601568057e+00 -4.4140032390724294e+01 2.3421941942726932e+01
|
||||
25 -3.4663429593560622e+01 3.0656489475121842e+00 -2.8305771699451558e+01
|
||||
26 2.6127823323623851e+01 4.0822835743217404e+01 4.2748889953099694e+00
|
||||
27 1.1011058517091254e+01 -4.6436458745736758e+01 1.8878846450788387e+01
|
||||
28 -4.0634774705109990e+01 1.5071357074236101e+01 -2.6829755184229253e+01
|
||||
29 3.0014317510846237e+01 3.1359613235965710e+01 7.9297758330981845e+00
|
||||
...
|
||||
|
|
|
|||
|
|
@ -469,6 +469,8 @@ TEST_F(FileOperationsTest, write_data)
|
|||
|
||||
TEST_FAILURE(".*ERROR: Cannot open file noexist.data: No such file or directory.*",
|
||||
command("read_data noexist.data"););
|
||||
TEST_FAILURE(".*ERROR: Unknown read_data keyword xxx.*",
|
||||
command("read_data noexist.data xxx"););
|
||||
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("pair_style zero 1.0");
|
||||
|
|
@ -501,6 +503,116 @@ TEST_F(FileOperationsTest, write_data)
|
|||
delete_file("triclinic.data");
|
||||
}
|
||||
|
||||
#define GETIDX(i) lmp->atom->map(i)
|
||||
TEST_F(FileOperationsTest, read_data_fix)
|
||||
{
|
||||
ASSERT_EQ(lmp->restart_ver, -1);
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("echo none");
|
||||
command("atom_modify map array");
|
||||
command("fix MoleculeIDs all property/atom mol");
|
||||
command("region box block -2 2 -2 2 -2 2");
|
||||
command("create_box 1 box");
|
||||
command("create_atoms 1 single 1.0 0.0 0.0");
|
||||
command("create_atoms 1 single 0.0 1.0 0.0");
|
||||
command("create_atoms 1 single 1.0 0.0 1.0");
|
||||
command("create_atoms 1 single 0.0 1.0 1.0");
|
||||
command("mass 1 1.0");
|
||||
command("set atom 1*2 mol 1");
|
||||
command("set atom 3*4 mol 2");
|
||||
command("write_data test_mol_id.data");
|
||||
lmp->atom->molecule[0] = 5;
|
||||
lmp->atom->molecule[1] = 6;
|
||||
lmp->atom->molecule[2] = 5;
|
||||
lmp->atom->molecule[3] = 6;
|
||||
lmp->atom->tag[0] = 9;
|
||||
lmp->atom->tag[1] = 6;
|
||||
lmp->atom->tag[2] = 7;
|
||||
lmp->atom->tag[3] = 8;
|
||||
lmp->atom->map_init(1);
|
||||
lmp->atom->map_set();
|
||||
command("write_data test_mol_id_merge.data");
|
||||
command("clear");
|
||||
END_HIDE_OUTPUT();
|
||||
TEST_FAILURE(".*ERROR: Cannot use read_data add before simulation box is defined.*",
|
||||
command("read_data test_mol_id.data add append"););
|
||||
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("atom_modify map array");
|
||||
command("fix MoleculeIDs all property/atom mol");
|
||||
command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules");
|
||||
command("read_data test_mol_id_merge.data add merge fix MoleculeIDs NULL Molecules");
|
||||
END_HIDE_OUTPUT();
|
||||
|
||||
EXPECT_EQ(lmp->atom->natoms, 8);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(6)], 6);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 5);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 6);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(9)], 5);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(6)], 6);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9);
|
||||
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("clear");
|
||||
command("atom_modify map array");
|
||||
command("fix MoleculeIDs all property/atom mol");
|
||||
command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules");
|
||||
command("read_data test_mol_id.data add append fix MoleculeIDs NULL Molecules");
|
||||
END_HIDE_OUTPUT();
|
||||
EXPECT_EQ(lmp->atom->natoms, 8);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(5)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(6)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 2);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(5)], 5);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(6)], 6);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8);
|
||||
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("clear");
|
||||
command("atom_modify map array");
|
||||
command("fix MoleculeIDs all property/atom mol");
|
||||
command("read_data test_mol_id.data fix MoleculeIDs NULL Molecules");
|
||||
command("read_data test_mol_id.data add 6 4 fix MoleculeIDs NULL Molecules");
|
||||
END_HIDE_OUTPUT();
|
||||
EXPECT_EQ(lmp->atom->natoms, 8);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(2)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(3)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(4)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(7)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(8)], 1);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(9)], 2);
|
||||
EXPECT_EQ(lmp->atom->molecule[GETIDX(10)], 2);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(1)], 1);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(2)], 2);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(3)], 3);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(4)], 4);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(7)], 7);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9);
|
||||
EXPECT_EQ(lmp->atom->tag[GETIDX(10)], 10);
|
||||
}
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
|
|
|
|||
Loading…
Reference in New Issue