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Merge branch 'master' into acks2_release

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This commit is contained in:
Axel Kohlmeyer
2021-10-11 09:58:44 -04:00
parent 277f7a7e51 ab51c1bd3d
commit 70cbb72e42
34 changed files with 526 additions and 561 deletions
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5
cmake/CMakeLists.txt
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@ -90,8 +90,11 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
endif()
endif()
# we require C++11 without extensions
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
set(CMAKE_CXX_STANDARD 11)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hack for MSVC which by default always reports an old C++ standard in the __cplusplus macro

2
cmake/Modules/Packages/KOKKOS.cmake
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@ -1,7 +1,7 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
if(CMAKE_CXX_STANDARD LESS 14)
set(CMAKE_CXX_STANDARD 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS

5
cmake/Modules/Packages/MACHDYN.cmake
View File

@ -7,8 +7,9 @@ endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
mark_as_advanced(EIGEN3_URL)
mark_as_advanced(EIGEN3_MD5)
include(ExternalProject)

80
doc/src/Howto_thermostat.rst
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@ -2,8 +2,8 @@ Thermostats
===========
Thermostatting means controlling the temperature of particles in an MD
simulation. :doc:`Barostatting <Howto_barostat>` means controlling the
pressure. Since the pressure includes a kinetic component due to
simulation. :doc:`Barostatting <Howto_barostat>` means controlling
the pressure. Since the pressure includes a kinetic component due to
particle velocities, both these operations require calculation of the
temperature. Typically a target temperature (T) and/or pressure (P)
is specified by the user, and the thermostat or barostat attempts to
@ -26,11 +26,13 @@ can be invoked via the *dpd/tstat* pair style:
* :doc:`pair_style dpd/tstat <pair_dpd>`
:doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the :doc:`Howto nemd <Howto_nemd>` page for further details. :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
particles.
particles. :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
except that it subtracts out a velocity bias due to a deforming box
and integrates the SLLOD equations of motion. See the :doc:`Howto
nemd <Howto_nemd>` page for further details. :doc:`Fix nvt/sphere
<fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>`
thermostat not only translation velocities but also rotational
velocities for spherical and aspherical particles.
.. note::
@ -40,25 +42,31 @@ particles.
e.g. molecular systems. The latter can be tricky to do correctly.
DPD thermostatting alters pairwise interactions in a manner analogous
to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
to the per-particle thermostatting of :doc:`fix langevin
<fix_langevin>`.
Any of the thermostatting fixes can be instructed to use custom temperature
computes that remove bias which has two effects: first, the current
calculated temperature, which is compared to the requested target temperature,
is calculated with the velocity bias removed; second, the thermostat adjusts
only the thermal temperature component of the particle's velocities, which are
the velocities with the bias removed. The removed bias is then added back
to the adjusted velocities. See the doc pages for the individual
fixes and for the :doc:`fix_modify <fix_modify>` command for
instructions on how to assign a temperature compute to a
thermostatting fix. For example, you can apply a thermostat to only
the x and z components of velocity by using it in conjunction with
:doc:`compute temp/partial <compute_temp_partial>`. Of you could
thermostat only the thermal temperature of a streaming flow of
particles without affecting the streaming velocity, by using
:doc:`compute temp/profile <compute_temp_profile>`.
Any of the thermostatting fixes can be instructed to use custom
temperature computes that remove bias which has two effects: first,
the current calculated temperature, which is compared to the requested
target temperature, is calculated with the velocity bias removed;
second, the thermostat adjusts only the thermal temperature component
of the particle's velocities, which are the velocities with the bias
removed. The removed bias is then added back to the adjusted
velocities. See the doc pages for the individual fixes and for the
:doc:`fix_modify <fix_modify>` command for instructions on how to
assign a temperature compute to a thermostatting fix.
Below is a list of some custom temperature computes that can be used like that:
For example, you can apply a thermostat only to atoms in a spatial
region by using it in conjunction with :doc:`compute temp/region
<compute_temp_region>`. Or you can apply a thermostat to only the x
and z components of velocity by using it with :doc:`compute
temp/partial <compute_temp_partial>`. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using :doc:`compute temp/profile
<compute_temp_profile>`.
Below is a list of custom temperature computes that can be used like
that:
* :doc:`compute_temp_asphere`
* :doc:`compute_temp_body`
@ -72,8 +80,6 @@ Below is a list of some custom temperature computes that can be used like that:
* :doc:`compute_temp_rotate`
* :doc:`compute_temp_sphere`
.. note::
Only the nvt fixes perform time integration, meaning they update
@ -86,17 +92,17 @@ Below is a list of some custom temperature computes that can be used like that:
* :doc:`fix nve/sphere <fix_nve_sphere>`
* :doc:`fix nve/asphere <fix_nve_asphere>`
Thermodynamic output, which can be setup via the
:doc:`thermo_style <thermo_style>` command, often includes temperature
values. As explained on the page for the
:doc:`thermo_style <thermo_style>` command, the default temperature is
setup by the thermo command itself. It is NOT the temperature
associated with any thermostatting fix you have defined or with any
compute you have defined that calculates a temperature. The doc pages
for the thermostatting fixes explain the ID of the temperature compute
they create. Thus if you want to view these temperatures, you need to
specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command. Or you can use the
:doc:`thermo_modify <thermo_modify>` command to re-define what
Thermodynamic output, which can be setup via the :doc:`thermo_style
<thermo_style>` command, often includes temperature values. As
explained on the page for the :doc:`thermo_style <thermo_style>`
command, the default temperature is setup by the thermo command
itself. It is NOT the temperature associated with any thermostatting
fix you have defined or with any compute you have defined that
calculates a temperature. The doc pages for the thermostatting fixes
explain the ID of the temperature compute they create. Thus if you
want to view these temperatures, you need to specify them explicitly
via the :doc:`thermo_style custom <thermo_style>` command. Or you can
use the :doc:`thermo_modify <thermo_modify>` command to re-define what
temperature compute is used for default thermodynamic output.
----------

25
doc/src/fix_langevin.rst
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@ -138,16 +138,18 @@ temperature with optional time-dependence as well.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. removing the center-of-mass velocity from a
group of atoms or removing the x-component of velocity from the
calculation. This is not done by default, but only if the
:doc:`fix_modify <fix_modify>` command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual :doc:`compute commands <compute>` to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
The *damp* parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0 means
@ -183,7 +185,8 @@ omega (which is derived from the angular momentum in the case of
aspherical particles).
The rotational temperature of the particles can be monitored by the
:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute
temp/asphere <compute_temp_asphere>` commands with their rotate
options.
For the *omega* keyword there is also a scale factor of

25
doc/src/fix_langevin_drude.rst
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@ -167,17 +167,20 @@ functions, and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.
Like other fixes that perform thermostatting, this fix can be used with
:doc:`compute commands <compute>` that remove a "bias" from the atom
velocities. E.g. removing the center-of-mass velocity from a group of
atoms. This is not done by default, but only if the
:doc:`fix_modify <fix_modify>` command is used to assign a temperature
compute to this fix that includes such a bias term. See the doc pages
for individual :doc:`compute commands <compute>` to determine which ones
include a bias. In this case, the thermostat works in the following
manner: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in. NOTE: this feature has not been tested.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
Note: The temperature thermostatting the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the

27
doc/src/fix_nh.rst
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@ -486,19 +486,20 @@ temperature or pressure during thermodynamic output via the
compute-ID. It also means that changing attributes of *thermo_temp*
or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, fix nvt and fix npt can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

30
doc/src/fix_npt_asphere.rst
View File

@ -48,8 +48,9 @@ can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command. See, for example, discussion of the *temp*,
*iso*, *aniso*, and *dilate* keywords.
specified by keywords and values documented with the :doc:`fix npt
<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
*aniso*, and *dilate* keywords.
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -89,18 +90,19 @@ It also means that changing attributes of *thermo_temp* or
*thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_npt_body.rst
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@ -87,18 +87,19 @@ It also means that changing attributes of *thermo_temp* or
*thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

27
doc/src/fix_npt_cauchy.rst
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@ -400,19 +400,20 @@ temperature or pressure during thermodynamic output via the
compute-ID. It also means that changing attributes of *thermo_temp*
or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, fix npt/cauchy can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_npt_sphere.rst
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@ -103,18 +103,19 @@ appropriate compute-ID. It also means that changing attributes of
*thermo_temp* or *thermo_press* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_asphere.rst
View File

@ -72,18 +72,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_body.rst
View File

@ -69,18 +69,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

74
doc/src/fix_nvt_sllod.rst
View File

@ -37,15 +37,16 @@ trajectory consistent with the canonical ensemble.
This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the :doc:`fix deform <fix_deform>` command, so each point in the simulation box
can be thought of as having a "streaming" velocity. This
position-dependent streaming velocity is subtracted from each atom's
actual velocity to yield a thermal velocity which is used for
temperature computation and thermostatting. For example, if the box
is being sheared in x, relative to y, then points at the bottom of the
box (low y) have a small x velocity, while points at the top of the
box (hi y) have a large x velocity. These velocities do not
contribute to the thermal "temperature" of the atom.
The size/shape change is induced by use of the :doc:`fix deform
<fix_deform>` command, so each point in the simulation box can be
thought of as having a "streaming" velocity. This position-dependent
streaming velocity is subtracted from each atom's actual velocity to
yield a thermal velocity which is used for temperature computation and
thermostatting. For example, if the box is being sheared in x,
relative to y, then points at the bottom of the box (low y) have a
small x velocity, while points at the top of the box (hi y) have a
large x velocity. These velocities do not contribute to the thermal
"temperature" of the atom.
.. note::
@ -60,13 +61,15 @@ contribute to the thermal "temperature" of the atom.
consistent.
The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent to
Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate the desired
velocity gradient and the correct production of work by stresses for
all forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`. As
implemented in LAMMPS, they are coupled to a Nose/Hoover chain
thermostat in a velocity Verlet formulation, closely following the
implementation used for the :doc:`fix nvt <fix_nh>` command.
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
equivalent to Newton's equations of motion for shear flow by
:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
the desired velocity gradient and the correct production of work by
stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
<Daivis>`. As implemented in LAMMPS, they are coupled to a
Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
following the implementation used for the :doc:`fix nvt <fix_nh>`
command.
.. note::
@ -94,27 +97,28 @@ underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
:doc:`compute_modify <compute_modify>` command or print this temperature
during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
the :doc:`thermo_style <thermo_style>` command) with ID =
*thermo_temp*. This means you can change the attributes of this fix's
temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
<compute_modify>` command or print this temperature during
thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
command using the appropriate compute-ID. It also means that changing
attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_nvt_sphere.rst
View File

@ -86,18 +86,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

25
doc/src/fix_temp_berendsen.rst
View File

@ -102,18 +102,19 @@ It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

41
doc/src/fix_temp_csvr.rst
View File

@ -110,28 +110,29 @@ during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` co
It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
Like other fixes that perform thermostatting, these fixes can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
An important feature of these thermostats is that they have an
associated effective energy that is a constant of motion.
The effective energy is the total energy (kinetic + potential) plus
the accumulated kinetic energy changes due to the thermostat. The
latter quantity is the global scalar computed by these fixes. This
feature is useful to check the integration of the equations of motion
against discretization errors. In other words, the conservation of
the effective energy can be used to choose an appropriate integration
associated effective energy that is a constant of motion. The
effective energy is the total energy (kinetic + potential) plus the
accumulated kinetic energy changes due to the thermostat. The latter
quantity is the global scalar computed by these fixes. This feature is
useful to check the integration of the equations of motion against
discretization errors. In other words, the conservation of the
effective energy can be used to choose an appropriate integration
:doc:`timestep <timestep>`. This is similar to the usual paradigm of
checking the conservation of the total energy in the microcanonical
ensemble.

26
doc/src/fix_temp_rescale.rst
View File

@ -109,19 +109,19 @@ command using the appropriate compute-ID. It also means that changing
attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the :doc:`fix_modify <fix_modify>` command is
used to assign a temperature compute to this fix that includes such a
bias term. See the doc pages for individual :doc:`compute commands
<compute>` to determine which ones include a bias. In this case, the
thermostat works in the following manner: the current temperature is
calculated taking the bias into account, bias is removed from each
atom, thermostatting is performed on the remaining thermal degrees of
freedom, and the bias is added back in.
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
----------

40
doc/src/fix_tgnh_drude.rst
View File

@ -187,26 +187,32 @@ barostatting.
----------
Like other fixes that perform thermostatting, these fixes can
be used with :doc:`compute commands <compute>` that calculate a
temperature after removing a "bias" from the atom velocities.
This is not done by default, but only if the :doc:`fix_modify <fix_modify>` command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal DOF, and the bias is added back in.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
atom velocities. E.g. to apply the thermostat only to atoms within a
spatial :doc:`region <region>`, or to remove the center-of-mass
velocity from a group of atoms, or to remove the x-component of
velocity from the calculation.
This is not done by default, but only if the :doc:`fix_modify
<fix_modify>` command is used to assign a temperature compute to this
fix that includes such a bias term. See the doc pages for individual
:doc:`compute temp commands <compute>` to determine which ones include
a bias. In this case, the thermostat works in the following manner:
bias is removed from each atom, thermostatting is performed on the
remaining thermal degrees of freedom, and the bias is added back in.
.. note::
However, not all temperature compute commands are valid to be used with these fixes.
Precisely, only temperature compute that does not modify the DOF of the group can be used.
E.g. :doc:`compute temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos <compute_viscosity_cos>`
compute the kinetic energy after remove a velocity gradient without affecting the DOF of the group,
then they can be invoked in this way.
In contrast, :doc:`compute temp/partial <compute_temp_partial>` may remove the DOF at one or more dimensions,
therefore it cannot be used with these fixes.
However, not all temperature compute commands are valid to be used
with these fixes. Precisely, only temperature compute that does
not modify the DOF of the group can be used. E.g. :doc:`compute
temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos
<compute_viscosity_cos>` compute the kinetic energy after remove a
velocity gradient without affecting the DOF of the group, then they
can be invoked in this way. In contrast, :doc:`compute
temp/partial <compute_temp_partial>` may remove the DOF at one or
more dimensions, therefore it cannot be used with these fixes.
----------

12
doc/utils/requirements.txt
View File

@ -1,7 +1,7 @@
Sphinx==4.0.3
sphinxcontrib-spelling==7.2.1
Sphinx
sphinxcontrib-spelling
git+git://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs==3.2.0
breathe==4.31.0
Pygments==2.10.0
six==1.16.0
sphinx_tabs
breathe
Pygments
six

7
lib/machdyn/Install.py
View File

@ -17,11 +17,12 @@ parser = ArgumentParser(prog='Install.py',
# settings
version = '3.3.9'
version = '3.4.0'
tarball = "eigen.tar.gz"
# known checksums for different Eigen versions. used to validate the download.
checksums = { \
'3.4.0' : '4c527a9171d71a72a9d4186e65bea559', \
'3.3.9' : '609286804b0f79be622ccf7f9ff2b660', \
'3.3.7' : '9e30f67e8531477de4117506fe44669b' \
}
@ -35,7 +36,7 @@ Syntax from src dir: make lib-smd args="-b"
Syntax from lib dir: python Install.py -b
or: python Install.py -p /usr/include/eigen3"
or: python Install.py -v 3.3.7 -b
or: python Install.py -v 3.4.0 -b
Example:
@ -77,7 +78,7 @@ if pathflag:
if buildflag:
print("Downloading Eigen ...")
eigentar = os.path.join(homepath, tarball)
url = "https://gitlab.com/libeigen/eigen/-/archive/%s/eigen-%s.tar.gz" % (version,version)
url = "https://download.lammps.org/thirdparty/eigen-%s.tar.gz" % version
geturl(url, eigentar)
# verify downloaded archive integrity via md5 checksum, if known.

16
src/.gitignore vendored
View File

@ -27,6 +27,9 @@
/*_ssa.h
/*_ssa.cpp
!accelerator_kokkos.h
!accelerator_omp.h
/fix_mdi_engine.cpp
/fix_mdi_engine.h
/library_mdi.cpp
@ -202,7 +205,6 @@
/plugin.cpp
/plugin.h
/lammpsplugin.h
/atom_vec_spin.cpp
/atom_vec_spin.h
@ -265,8 +267,6 @@
/fix_drag.h
/fix_numdiff.cpp
/fix_numdiff.h
/fix_nve_noforce.cpp
/fix_nve_noforce.h
/fix_spring_rg.cpp
/fix_spring_rg.h
/fix_temp_csld.cpp
@ -367,8 +367,6 @@
/atom_vec_dpd.h
/atom_vec_electron.cpp
/atom_vec_electron.h
/atom_vec_ellipsoid.cpp
/atom_vec_ellipsoid.h
/atom_vec_full.cpp
/atom_vec_full.h
/atom_vec_full_hars.cpp
@ -535,8 +533,6 @@
/dihedral_harmonic.h
/dihedral_helix.cpp
/dihedral_helix.h
/dihedral_hybrid.cpp
/dihedral_hybrid.h
/dihedral_multi_harmonic.cpp
/dihedral_multi_harmonic.h
/dihedral_nharmonic.cpp
@ -885,8 +881,6 @@
/fix_widom.cpp
/fix_widom.h
/gpu_extra.h
/gridcomm.cpp
/gridcomm.h
/group_ndx.cpp
/group_ndx.h
/gz_file_writer.cpp
@ -911,8 +905,6 @@
/improper_fourier.h
/improper_harmonic.cpp
/improper_harmonic.h
/improper_hybrid.cpp
/improper_hybrid.h
/improper_inversion_harmonic.cpp
/improper_inversion_harmonic.h
/improper_ring.cpp
@ -1334,8 +1326,6 @@
/thr_data.h
/verlet_split.cpp
/verlet_split.h
/write_dump.cpp
/write_dump.h
/xdr_compat.cpp
/xdr_compat.h
/zstd_file_writer.cpp

4
src/DPD-REACT/random_external_state.h
View File

@ -78,8 +78,8 @@
namespace random_external_state {
typedef uint64_t es_RNG_t;
enum { MAX_URAND = 0xffffffffU };
enum { MAX_URAND64 = 0xffffffffffffffffULL - 1 };
constexpr uint32_t MAX_URAND = 0xffffffffU;
constexpr uint64_t MAX_URAND64 = 0xffffffffffffffffULL - 1;
LAMMPS_INLINE
uint32_t es_urand(es_RNG_t &state_)

189
src/EXTRA-MOLECULE/angle_gaussian.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -34,9 +33,9 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
AngleGaussian::AngleGaussian(LAMMPS *lmp)
: Angle(lmp), nterms(nullptr), angle_temperature(nullptr),
alpha(nullptr), width(nullptr), theta0(nullptr)
AngleGaussian::AngleGaussian(LAMMPS *lmp) :
Angle(lmp), nterms(nullptr), angle_temperature(nullptr), alpha(nullptr), width(nullptr),
theta0(nullptr)
{
}
@ -49,13 +48,13 @@ AngleGaussian::~AngleGaussian()
memory->destroy(nterms);
memory->destroy(angle_temperature);
for (int i = 1; i <= atom->nangletypes; i++) {
delete [] alpha[i];
delete [] width[i];
delete [] theta0[i];
delete[] alpha[i];
delete[] width[i];
delete[] theta0[i];
}
delete [] alpha;
delete [] width;
delete [] theta0;
delete[] alpha;
delete[] width;
delete[] theta0;
}
}
@ -63,15 +62,15 @@ AngleGaussian::~AngleGaussian()
void AngleGaussian::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
int i1, i2, i3, n, type;
double delx1, dely1, delz1, delx2, dely2, delz2;
double eangle, f1[3], f3[3];
double dtheta;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
double prefactor, exponent, g_i, sum_g_i, sum_numerator;
eangle = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -92,7 +91,7 @@ void AngleGaussian::compute(int eflag, int vflag)
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
r1 = sqrt(rsq1);
// 2nd bond
@ -101,20 +100,20 @@ void AngleGaussian::compute(int eflag, int vflag)
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
c /= r1 * r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
s = sqrt(1.0 - c * c);
if (s < SMAL) s = SMAL;
s = 1.0/s;
s = 1.0 / s;
// force & energy
double theta = acos(c);
@ -123,28 +122,28 @@ void AngleGaussian::compute(int eflag, int vflag)
sum_numerator = 0.0;
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]);
g_i = prefactor*exp(exponent);
prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
exponent = -2 * 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]);
sum_numerator += g_i * dtheta / (width[type][i] * width[type][i]);
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (eflag) eangle = -(force->boltz*angle_temperature[type])*log(sum_g_i);
if (eflag) eangle = -(force->boltz * angle_temperature[type]) * log(sum_g_i);
// I should check about the sign of this expression
a = -4.0*(force->boltz*angle_temperature[type])*(sum_numerator/sum_g_i)*s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
a = -4.0 * (force->boltz * angle_temperature[type]) * (sum_numerator / sum_g_i) * s;
a11 = a * c / rsq1;
a12 = -a / (r1 * r2);
a22 = a * c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
f1[0] = a11 * delx1 + a12 * delx2;
f1[1] = a11 * dely1 + a12 * dely2;
f1[2] = a11 * delz1 + a12 * delz2;
f3[0] = a22 * delx2 + a12 * delx1;
f3[1] = a22 * dely2 + a12 * dely1;
f3[2] = a22 * delz2 + a12 * delz1;
// apply force to each of 3 atoms
@ -166,8 +165,9 @@ void AngleGaussian::compute(int eflag, int vflag)
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
if (evflag)
ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
delz2);
}
}
@ -176,20 +176,20 @@ void AngleGaussian::compute(int eflag, int vflag)
void AngleGaussian::allocate()
{
allocated = 1;
int n = atom->nangletypes;
int n = atom->nangletypes + 1;
memory->create(nterms,n+1,"angle:nterms");
memory->create(angle_temperature,n+1,"angle:angle_temperature");
memory->create(nterms, n, "angle:nterms");
memory->create(angle_temperature, n, "angle:angle_temperature");
alpha = new double *[n+1];
width = new double *[n+1];
theta0 = new double *[n+1];
memset(alpha,0,sizeof(double)*(n+1));
memset(width,0,sizeof(double)*(n+1));
memset(theta0,0,sizeof(double)*(n+1));
alpha = new double *[n];
width = new double *[n];
theta0 = new double *[n];
memset(alpha, 0, sizeof(double *) * n);
memset(width, 0, sizeof(double *) * n);
memset(theta0, 0, sizeof(double *) * n);
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
memory->create(setflag, n, "angle:setflag");
memset(setflag, 0, sizeof(int) * n);
}
/* ----------------------------------------------------------------------
@ -198,15 +198,14 @@ void AngleGaussian::allocate()
void AngleGaussian::coeff(int narg, char **arg)
{
if (narg < 6) error->all(FLERR,"Incorrect args for angle coefficients");
if (narg < 6) error->all(FLERR, "Incorrect args for angle coefficients");
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,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");
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 (!allocated) allocate();
@ -217,21 +216,21 @@ void AngleGaussian::coeff(int narg, char **arg)
angle_temperature[i] = angle_temperature_one;
nterms[i] = n;
delete[] alpha[i];
alpha[i] = new double [n];
alpha[i] = new double[n];
delete[] width[i];
width[i] = new double [n];
width[i] = new double[n];
delete[] theta0[i];
theta0[i] = new double [n];
theta0[i] = new double[n];
for (int j = 0; j < n; j++) {
alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
theta0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp)* MY_PI / 180.0;
alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
theta0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp) * MY_PI / 180.0;
setflag[i] = 1;
}
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
if (count == 0) error->all(FLERR, "Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
@ -247,12 +246,12 @@ double AngleGaussian::equilibrium_angle(int i)
void AngleGaussian::write_restart(FILE *fp)
{
fwrite(&angle_temperature[1],sizeof(double),atom->nangletypes,fp);
fwrite(&nterms[1],sizeof(int),atom->nangletypes,fp);
fwrite(&angle_temperature[1], sizeof(double), atom->nangletypes, fp);
fwrite(&nterms[1], sizeof(int), atom->nangletypes, fp);
for (int i = 1; i <= atom->nangletypes; i++) {
fwrite(alpha[i],sizeof(double),nterms[i],fp);
fwrite(width[i],sizeof(double),nterms[i],fp);
fwrite(theta0[i],sizeof(double),nterms[i],fp);
fwrite(alpha[i], sizeof(double), nterms[i], fp);
fwrite(width[i], sizeof(double), nterms[i], fp);
fwrite(theta0[i], sizeof(double), nterms[i], fp);
}
}
@ -265,31 +264,32 @@ void AngleGaussian::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&angle_temperature[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nangletypes,fp,nullptr,error);
utils::sfread(FLERR, &angle_temperature[1], sizeof(double), atom->nangletypes, fp, nullptr,
error);
utils::sfread(FLERR, &nterms[1], sizeof(int), atom->nangletypes, fp, nullptr, error);
}
MPI_Bcast(&angle_temperature[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&nterms[1],atom->nangletypes,MPI_INT,0,world);
MPI_Bcast(&angle_temperature[1], atom->nangletypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&nterms[1], atom->nangletypes, MPI_INT, 0, world);
// allocate
for (int i = 1; i <= atom->nangletypes; i++) {
alpha[i] = new double [nterms[i]];
width[i] = new double [nterms[i]];
theta0[i] = new double [nterms[i]];
alpha[i] = new double[nterms[i]];
width[i] = new double[nterms[i]];
theta0[i] = new double[nterms[i]];
}
if (comm->me == 0) {
for (int i = 1; i <= atom->nangletypes; i++) {
utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,theta0[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR, alpha[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR, width[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR, theta0[i], sizeof(double), nterms[i], fp, nullptr, error);
}
}
for (int i = 1; i <= atom->nangletypes; i++) {
MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta0[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(alpha[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(width[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(theta0[i], nterms[i], MPI_DOUBLE, 0, world);
}
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
@ -302,13 +302,12 @@ void AngleGaussian::read_restart(FILE *fp)
void AngleGaussian::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++) {
fprintf(fp,"%d %g %d",i,angle_temperature[i],nterms[i]);
fprintf(fp, "%d %g %d", i, angle_temperature[i], nterms[i]);
for (int j = 0; j < nterms[i]; j++) {
fprintf(fp," %g %g %g",alpha[i][j],width[i][j],(theta0[i][j]/MY_PI)*180.0);
fprintf(fp, " %g %g %g", alpha[i][j], width[i][j], (theta0[i][j] / MY_PI) * 180.0);
}
fprintf(fp, "\n");
}
}
/* ---------------------------------------------------------------------- */
@ -320,30 +319,30 @@ double AngleGaussian::single(int type, int i1, int i2, int i3)
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
domain->minimum_image(delx1, dely1, delz1);
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
domain->minimum_image(delx2, dely2, delz2);
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
c /= r1 * r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double theta = acos(c) ;
double theta = acos(c);
double sum_g_i = 0.0;
for (int i = 0; i < nterms[type]; i++) {
double dtheta = theta - theta0[type][i];
double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
double exponent = -2*dtheta*dtheta/(width[type][i]*width[type][i]);
double g_i = prefactor*exp(exponent);
double prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
double exponent = -2 * dtheta * dtheta / (width[type][i] * width[type][i]);
double g_i = prefactor * exp(exponent);
sum_g_i += g_i;
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
return -(force->boltz*angle_temperature[type])*log(sum_g_i);
return -(force->boltz * angle_temperature[type]) * log(sum_g_i);
}

182
src/EXTRA-MOLECULE/bond_gaussian.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,16 +13,16 @@
#include "bond_gaussian.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "neighbor.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -32,9 +31,9 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
BondGaussian::BondGaussian(LAMMPS *lmp)
: Bond(lmp), nterms(nullptr), bond_temperature(nullptr),
alpha(nullptr), width(nullptr), r0(nullptr)
BondGaussian::BondGaussian(LAMMPS *lmp) :
Bond(lmp), nterms(nullptr), bond_temperature(nullptr), alpha(nullptr), width(nullptr),
r0(nullptr)
{
reinitflag = 1;
}
@ -48,13 +47,13 @@ BondGaussian::~BondGaussian()
memory->destroy(nterms);
memory->destroy(bond_temperature);
for (int i = 1; i <= atom->nbondtypes; i++) {
delete [] alpha[i];
delete [] width[i];
delete [] r0[i];
delete[] alpha[i];
delete[] width[i];
delete[] r0[i];
}
delete [] alpha;
delete [] width;
delete [] r0;
delete[] alpha;
delete[] width;
delete[] r0;
}
}
@ -62,13 +61,13 @@ BondGaussian::~BondGaussian()
void BondGaussian::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r,dr;
int i1, i2, n, type;
double delx, dely, delz, ebond, fbond;
double rsq, r, dr;
double prefactor, exponent, g_i, sum_g_i, sum_numerator;
ebond = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -86,43 +85,45 @@ void BondGaussian::compute(int eflag, int vflag)
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
r = sqrt(rsq);
sum_g_i = 0.0;
sum_numerator = 0.0;
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]);
g_i = prefactor*exp(exponent);
prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
exponent = -2 * 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]);
sum_numerator += g_i * dr / (width[type][i] * width[type][i]);
}
// force & energy
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (r > 0.0) fbond = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
else fbond = 0.0;
if (r > 0.0)
fbond = -4.0 * (force->boltz * bond_temperature[type]) * (sum_numerator / sum_g_i) / r;
else
fbond = 0.0;
if (eflag) ebond = -(force->boltz*bond_temperature[type])*log(sum_g_i);
if (eflag) ebond = -(force->boltz * bond_temperature[type]) * log(sum_g_i);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1][0] += delx * fbond;
f[i1][1] += dely * fbond;
f[i1][2] += delz * fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2][0] -= delx * fbond;
f[i2][1] -= dely * fbond;
f[i2][2] -= delz * fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
}
}
@ -131,20 +132,20 @@ void BondGaussian::compute(int eflag, int vflag)
void BondGaussian::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
int n = atom->nbondtypes + 1;
memory->create(nterms,n+1,"bond:nterms");
memory->create(bond_temperature,n+1,"bond:bond_temperature");
memory->create(nterms, n, "bond:nterms");
memory->create(bond_temperature, n, "bond:bond_temperature");
alpha = new double *[n+1];
width = new double *[n+1];
r0 = new double *[n+1];
memset(alpha,0,sizeof(double)*(n+1));
memset(width,0,sizeof(double)*(n+1));
memset(r0,0,sizeof(double)*(n+1));
alpha = new double *[n];
width = new double *[n];
r0 = new double *[n];
memset(alpha, 0, sizeof(double *) * n);
memset(width, 0, sizeof(double *) * n);
memset(r0, 0, sizeof(double *) * n);
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
memory->create(setflag, n, "bond:setflag");
memset(setflag, 0, sizeof(int) * n);
}
/* ----------------------------------------------------------------------
@ -153,15 +154,14 @@ void BondGaussian::allocate()
void BondGaussian::coeff(int narg, char **arg)
{
if (narg < 6) error->all(FLERR,"Incorrect args for bond coefficients");
if (narg < 6) error->all(FLERR, "Incorrect args for bond coefficients");
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,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");
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 (!allocated) allocate();
@ -170,21 +170,21 @@ void BondGaussian::coeff(int narg, char **arg)
bond_temperature[i] = bond_temp_one;
nterms[i] = n;
delete[] alpha[i];
alpha[i] = new double [n];
alpha[i] = new double[n];
delete[] width[i];
width[i] = new double [n];
width[i] = new double[n];
delete[] r0[i];
r0[i] = new double [n];
r0[i] = new double[n];
for (int j = 0; j < n; j++) {
alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
r0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp);
alpha[i][j] = utils::numeric(FLERR, arg[3 + 3 * j], false, lmp);
width[i][j] = utils::numeric(FLERR, arg[4 + 3 * j], false, lmp);
r0[i][j] = utils::numeric(FLERR, arg[5 + 3 * j], false, lmp);
setflag[i] = 1;
}
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
@ -202,12 +202,12 @@ double BondGaussian::equilibrium_distance(int i)
void BondGaussian::write_restart(FILE *fp)
{
fwrite(&bond_temperature[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&nterms[1],sizeof(int),atom->nbondtypes,fp);
fwrite(&bond_temperature[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&nterms[1], sizeof(int), atom->nbondtypes, fp);
for (int i = 1; i <= atom->nbondtypes; i++) {
fwrite(alpha[i],sizeof(double),nterms[i],fp);
fwrite(width[i],sizeof(double),nterms[i],fp);
fwrite(r0[i],sizeof(double),nterms[i],fp);
fwrite(alpha[i], sizeof(double), nterms[i], fp);
fwrite(width[i], sizeof(double), nterms[i], fp);
fwrite(r0[i], sizeof(double), nterms[i], fp);
}
}
@ -220,31 +220,32 @@ void BondGaussian::read_restart(FILE *fp)
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&bond_temperature[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nbondtypes,fp,nullptr,error);
utils::sfread(FLERR, &bond_temperature[1], sizeof(double), atom->nbondtypes, fp, nullptr,
error);
utils::sfread(FLERR, &nterms[1], sizeof(int), atom->nbondtypes, fp, nullptr, error);
}
MPI_Bcast(&bond_temperature[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&nterms[1],atom->nbondtypes,MPI_INT,0,world);
MPI_Bcast(&bond_temperature[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
MPI_Bcast(&nterms[1], atom->nbondtypes, MPI_INT, 0, world);
// allocate
for (int i = 1; i <= atom->nbondtypes; i++) {
alpha[i] = new double [nterms[i]];
width[i] = new double [nterms[i]];
r0[i] = new double [nterms[i]];
alpha[i] = new double[nterms[i]];
width[i] = new double[nterms[i]];
r0[i] = new double[nterms[i]];
}
if (comm->me == 0) {
for (int i = 1; i <= atom->nbondtypes; i++) {
utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,r0[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR, alpha[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR, width[i], sizeof(double), nterms[i], fp, nullptr, error);
utils::sfread(FLERR, r0[i], sizeof(double), nterms[i], fp, nullptr, error);
}
}
for (int i = 1; i <= atom->nbondtypes; i++) {
MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(r0[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(alpha[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(width[i], nterms[i], MPI_DOUBLE, 0, world);
MPI_Bcast(r0[i], nterms[i], MPI_DOUBLE, 0, world);
}
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
@ -257,9 +258,9 @@ void BondGaussian::read_restart(FILE *fp)
void BondGaussian::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++) {
fprintf(fp,"%d %g %d",i,bond_temperature[i],nterms[i]);
fprintf(fp, "%d %g %d", i, bond_temperature[i], nterms[i]);
for (int j = 0; j < nterms[i]; j++) {
fprintf(fp," %g %g %g",alpha[i][j],width[i][j],r0[i][j]);
fprintf(fp, " %g %g %g", alpha[i][j], width[i][j], r0[i][j]);
}
fprintf(fp, "\n");
}
@ -267,26 +268,25 @@ void BondGaussian::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
double BondGaussian::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
double BondGaussian::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
{
double r = sqrt(rsq);
fforce = 0;
double sum_g_i = 0.0;
double sum_numerator = 0.0;
for (int i = 0; i < nterms[type]; i++) {
double dr = r - r0[type][i];
double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
double exponent = -2*dr*dr/(width[type][i]*width[type][i]);
double g_i = prefactor*exp(exponent);
sum_g_i += g_i;
sum_numerator += g_i*dr/(width[type][i]*width[type][i]);
}
for (int i = 0; i < nterms[type]; i++) {
double dr = r - r0[type][i];
double prefactor = (alpha[type][i] / (width[type][i] * sqrt(MY_PI2)));
double exponent = -2 * dr * dr / (width[type][i] * width[type][i]);
double g_i = prefactor * exp(exponent);
sum_g_i += g_i;
sum_numerator += g_i * dr / (width[type][i] * width[type][i]);
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (r > 0.0) fforce = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
if (r > 0.0)
fforce = -4.0 * (force->boltz * bond_temperature[type]) * (sum_numerator / sum_g_i) / r;
return -(force->boltz*bond_temperature[type])*log(sum_g_i);
return -(force->boltz * bond_temperature[type]) * log(sum_g_i);
}

19
src/INTERLAYER/pair_drip.cpp
View File

@ -31,7 +31,6 @@
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
@ -241,17 +240,17 @@ void PairDRIP::read_file(char *filename)
nparams++;
}
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if (comm->me != 0) {
params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
}
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if (comm->me != 0) {
params = (Param *) memory->srealloc(params, maxparam * sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam * sizeof(Param), MPI_BYTE, 0, world);
memory->destroy(elem2param);
memory->create(elem2param, nelements, nelements, "pair:elem2param");
for (int i = 0; i < nelements; i++) {

4
src/KOKKOS/kokkos_type.h
View File

@ -25,7 +25,9 @@
#include <Kokkos_ScatterView.hpp>
#include <Kokkos_UnorderedMap.hpp>
enum{FULL=1u,HALFTHREAD=2u,HALF=4u};
constexpr int FULL = 1;
constexpr int HALFTHREAD = 2;
constexpr int HALF = 4;
#if defined(KOKKOS_ENABLE_CXX11)
#undef ISFINITE

16
src/MISC/fix_ipi.cpp
View File

@ -200,22 +200,10 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
hasdata = bsize = 0;
// creates a temperature compute for all atoms
char** newarg = new char*[3];
newarg[0] = (char *) "IPI_TEMP";
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
modify->add_compute("IPI_TEMP all temp");
// creates a pressure compute to extract the virial
newarg = new char*[5];
newarg[0] = (char *) "IPI_PRESS";
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = (char *) "IPI_TEMP";
newarg[4] = (char *) "virial";
modify->add_compute(5,newarg);
delete [] newarg;
modify->add_compute("IPI_PRESS all pressure IPI_TEMP virial");
// create instance of Irregular class
irregular = new Irregular(lmp);

26
src/PLUMED/fix_plumed.cpp
View File

@ -215,31 +215,13 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
// Define compute to calculate potential energy
id_pe = new char[8];
strcpy(id_pe,"plmd_pe");
char **newarg = new char*[3];
newarg[0] = id_pe;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pe";
modify->add_compute(3,newarg);
delete [] newarg;
int ipe = modify->find_compute(id_pe);
c_pe = modify->compute[ipe];
id_pe = utils::strdup("plmd_pe");
c_pe = modify->add_compute(std::string(id_pe) + " all pe");
// Define compute to calculate pressure tensor
id_press = new char[11];
strcpy(id_press,"plmd_press");
newarg = new char*[5];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = (char *) "NULL";
newarg[4] = (char *) "virial";
modify->add_compute(5,newarg);
delete [] newarg;
int ipress = modify->find_compute(id_press);
c_press = modify->compute[ipress];
id_press = utils::strdup("plmd_press");
c_press = modify->add_compute(std::string(id_press) + " all pressure NULL virial");
for (int i = 0; i < modify->nfix; i++) {
const char * const check_style = modify->fix[i]->style;

4
src/exceptions.h
View File

@ -35,8 +35,8 @@ class LAMMPSAbortException : public LAMMPSException {
public:
MPI_Comm universe;
LAMMPSAbortException(const std::string &msg, MPI_Comm universe) :
LAMMPSException(msg), universe(universe)
LAMMPSAbortException(const std::string &msg, MPI_Comm _universe) :
LAMMPSException(msg), universe(_universe)
{
}
};

6
src/lammpsplugin.h
View File

@ -15,8 +15,9 @@
#define LMP_LAMMPSPLUGIN_H
// C style API and data structure required for dynamic loading
#ifdef __cplusplus
extern "C" {
#endif
typedef void *(lammpsplugin_factory1) (void *);
typedef void *(lammpsplugin_factory2) (void *, int, char **);
@ -41,6 +42,9 @@ typedef void (*lammpsplugin_initfunc)(void *, void *, void *);
// to load a plugin; uses C bindings
void lammpsplugin_init(void *, void *, void *);
#ifdef __cplusplus
}
#endif
#endif

4
src/tokenizer.cpp
View File

@ -49,8 +49,8 @@ TokenizerException::TokenizerException(const std::string &msg, const std::string
* \param str string to be processed
* \param separators string with separator characters (default: " \t\r\n\f") */
Tokenizer::Tokenizer(const std::string &str, const std::string &separators) :
text(str), separators(separators), start(0), ntokens(std::string::npos)
Tokenizer::Tokenizer(const std::string &str, const std::string &_separators) :
text(str), separators(_separators), start(0), ntokens(std::string::npos)
{
// replace known UTF-8 characters with ASCII equivalents
if (utils::has_utf8(text)) text = utils::utf8_subst(text);

37
tools/singularity/README.md
View File

@ -10,12 +10,6 @@ workstation, e.g. when bugs are reported that can only be reproduced on
a specific OS or with specific (mostly older) versions of tools,
compilers, or libraries.
Ready-to-use container images built from some these definition files are
occasionally uploaded to the container library at sylabs.io. They
can be found here: https://cloud.sylabs.io/library/lammps/default/lammps_development#
and will be signed with a GPG key that has the fingerprint:
EEA103764C6C633EDC8AC428D9B44E93BF0C375A
Here is a workflow for testing a compilation of LAMMPS with a locally
built CentOS 7.x singularity container.
@ -30,34 +24,3 @@ cmake -C ../cmake/presets/most.cmake ../cmake
make
```
And here is the equivalent workflow for testing a compilation of LAMMPS
using a pre-built Ubuntu 18.04LTS singularity container.
```
cd some/work/directory
git clone --depth 500 git://github.com/lammps/lammps.git lammps
mkdir build-ubuntu18
cd build-ubuntu18
singularity pull library://lammps/default/lammps_development:ubuntu18.04
singularity exec lammps_development_ubuntu18.04.sif bash --login
cmake -C ../cmake/presets/most.cmake ../cmake
make
```
| Currently available: | Description |
| ------------------------------ | ---------------------------------------------- |
| centos7.def | CentOS 7.x with EPEL enabled, no LaTeX |
| centos8.def | CentOS 8.x with EPEL enabled |
| fedora34_mingw.def | Fedora 34 with MinGW cross-compiler toolchain |
| ubuntu16.04.def | Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX |
| ubuntu18.04.def | Ubuntu 18.04LTS with MPI == OpenMPI |
| ubuntu18.04_amd_rocm.def | Ubuntu 18.04LTS with AMD ROCm toolkit |
| ubuntu18.04_gpu.def | Ubuntu 18.04LTS with -"- plus Nvidia CUDA 11.0 |
| ubuntu18.04_nvidia.def | Ubuntu 18.04LTS with Nvidia CUDA 11.0 toolkit |
| ubuntu18.04_intel_opencl.def | Ubuntu 18.04LTS with Intel OpenCL runtime |
| ubuntu20.04.def | Ubuntu 20.04LTS with MPI == OpenMPI |
| ubuntu20.04_amd_rocm.def | Ubuntu 20.04LTS with AMD ROCm toolkit |
| ubuntu20.04_gpu.def | Ubuntu 20.04LTS with -"- plus Nvidia CUDA 11.0 |
| ubuntu20.04_nvidia.def | Ubuntu 20.04LTS with Nvidia CUDA 11.0 toolkit |
| ubuntu20.04_intel_opencl.def | Ubuntu 20.04LTS with Intel OpenCL runtime |
| ------------------------------ | ---------------------------------------------- |

4
unittest/python/python-capabilities.py
View File

@ -166,9 +166,9 @@ class PythonCapabilities(unittest.TestCase):
self.assertIn('single',settings['GPU']['precision'])
if self.cmake_cache['PKG_KOKKOS']:
if self.cmake_cache['Kokkos_ENABLE_OPENMP']:
if 'Kokkos_ENABLE_OPENMP' in self.cmake_cache and self.cmake_cache['Kokkos_ENABLE_OPENMP']:
self.assertIn('openmp',settings['KOKKOS']['api'])
if self.cmake_cache['Kokkos_ENABLE_SERIAL']:
if 'Kokkos_ENABLE_SERIAL' in self.cmake_cache and self.cmake_cache['Kokkos_ENABLE_SERIAL']:
self.assertIn('serial',settings['KOKKOS']['api'])
self.assertIn('double',settings['KOKKOS']['precision'])