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Update from upstream

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This commit is contained in:
Stan Gerald Moore
2022-01-31 16:31:46 -07:00
parent cd6df24e37 a6a2492282
commit fad47312e6
1804 changed files with 20765 additions and 14314 deletions
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3
cmake/CMakeLists.txt
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@ -339,7 +339,6 @@ pkg_depends(ML-IAP ML-SNAP)
pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(PHONON KSPACE)
pkg_depends(SCAFACOS MPI)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
@ -609,7 +608,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()

4
cmake/Modules/Packages/GPU.cmake
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@ -306,12 +306,12 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_COMPILER STREQUAL "clang")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
else()
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()

6
cmake/Modules/Packages/KOKKOS.cmake
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@ -109,6 +109,12 @@ if(PKG_KSPACE)
endif()
endif()
if(PKG_PHONON)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/third_order_kokkos.cpp)
endif()
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
# detects styles which have KOKKOS version

9
cmake/Modules/Packages/PHONON.cmake Normal file
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@ -0,0 +1,9 @@
# fix phonon may only be installed if also the FFT wrappers from KSPACE are installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/PHONON/fix_phonon.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "1" "14 December 2021" "2021-12-14"
.TH LAMMPS "1" "7 January 2022" "2022-1-7"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

5
doc/src/Bibliography.rst
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@ -1123,9 +1123,12 @@ Bibliography
**(Sun)**
Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Surblys)**
**(Surblys2019)**
Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2021)**
Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
**(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)

4
doc/src/Commands_all.rst
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@ -47,7 +47,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`dynamical_matrix (k) <dynamical_matrix>`
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
@ -117,7 +117,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`thermo <thermo>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`third_order <third_order>`
* :doc:`third_order (k) <third_order>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`

1
doc/src/Commands_compute.rst
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@ -28,6 +28,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`angle <compute_angle>`
* :doc:`angle/local <compute_angle_local>`
* :doc:`angmom/chunk <compute_angmom_chunk>`
* :doc:`ave/sphere/atom (k) <compute_ave_sphere_atom>`
* :doc:`basal/atom <compute_basal_atom>`
* :doc:`body/local <compute_body_local>`
* :doc:`bond <compute_bond>`

1
doc/src/Commands_fix.rst
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@ -129,6 +129,7 @@ OPT.
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`numdiff <fix_numdiff>`
* :doc:`numdiff/virial <fix_numdiff_virial>`
* :doc:`nve (giko) <fix_nve>`
* :doc:`nve/asphere (gi) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`

1
doc/src/Commands_pair.rst
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@ -119,6 +119,7 @@ OPT.
* :doc:`granular <pair_granular>`
* :doc:`gw <pair_gw>`
* :doc:`gw/zbl <pair_gw>`
* :doc:`harmonic/cut (o) <pair_harmonic_cut>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`

2
doc/src/Developer_org.rst
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@ -225,7 +225,7 @@ follows:
commands in an input script.
- The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
parent class is for non-bonded or pairwise forces, which in LAMMPS
also includes many-body forces such as the Tersoff 3-body potential if
those are computed by walking pairwise neighbor lists. The Bond,
Angle, Dihedral, Improper parent classes are styles for bonded

31
doc/src/Developer_utils.rst
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@ -56,11 +56,11 @@ String to number conversions with validity check
These functions should be used to convert strings to numbers. They are
are strongly preferred over C library calls like ``atoi()`` or
``atof()`` since they check if the **entire** provided string is a valid
``atof()`` since they check if the **entire** string is a valid
(floating-point or integer) number, and will error out instead of
silently returning the result of a partial conversion or zero in cases
where the string is not a valid number. This behavior allows to more
easily detect typos or issues when processing input files.
where the string is not a valid number. This behavior improves
detecting typos or issues when processing input files.
Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
will convert a string into a boolean and will only accept certain words.
@ -76,19 +76,34 @@ strings for compliance without conversion.
----------
.. doxygenfunction:: numeric
.. doxygenfunction:: numeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: inumeric
.. doxygenfunction:: numeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric
.. doxygenfunction:: inumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical
.. doxygenfunction:: bnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: bnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: tnumeric(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const std::string &str, bool do_abort, LAMMPS *lmp)
:project: progguide
.. doxygenfunction:: logical(const char *file, int line, const char *str, bool do_abort, LAMMPS *lmp)
:project: progguide

2
doc/src/Developer_write.rst
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@ -55,7 +55,7 @@ of each timestep. First of all, implement a constructor:
if (narg < 4)
error->all(FLERR,"Illegal fix print/vel command");
nevery = force->inumeric(FLERR,arg[3]);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0)
error->all(FLERR,"Illegal fix print/vel command");
}

10
doc/src/Errors_messages.rst
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@ -1941,6 +1941,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Compute ID for fix numdiff does not exist*
Self-explanatory.
*Compute ID for fix numdiff/virial does not exist*
Self-explanatory.
*Compute ID for fix store/state does not exist*
Self-explanatory.
@ -3796,6 +3799,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory. Efficient loop over all atoms for numerical
difference requires consecutive atom IDs.
*Fix numdiff/virial must use group all*
Virial contributions computed by this fix are
computed on all atoms.
*Fix nve/asphere requires extended particles*
This fix can only be used for particles with a shape setting.
@ -7772,9 +7779,6 @@ keyword to allow for additional bonds to be formed
The system size must fit in a 32-bit integer to use this dump
style.
*Too many atoms to dump sort*
Cannot sort when running with more than 2\^31 atoms.
*Too many elements extracted from MEAM library.*
Increase 'maxelt' in meam.h and recompile.

2
doc/src/Errors_warnings.rst
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@ -416,7 +416,7 @@ This will most likely cause errors in kinetic fluctuations.
not defined for the specified atom style.
*Molecule has bond topology but no special bond settings*
This means the bonded atoms will not be excluded in pair-wise
This means the bonded atoms will not be excluded in pairwise
interactions.
*Molecule template for create_atoms has multiple molecules*

38
doc/src/Modify_pair.rst
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@ -12,24 +12,24 @@ includes some optional methods to enable its use with rRESPA.
Here is a brief description of the class methods in pair.h:
+---------------------------------+-------------------------------------------------------------------+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+-------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
+---------------------------------+-------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+-------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+-------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+-------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+-------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+-------------------------------------------------------------------+
| single | force and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+-------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+-------------------------------------------------------------------+
+---------------------------------+---------------------------------------------------------------------+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+---------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
+---------------------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+---------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+---------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+---------------------------------------------------------------------+
The inner/middle/outer routines are optional.

34
doc/src/Modify_style.rst
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@ -305,6 +305,40 @@ you are uncertain, please ask.
FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
convenience function where possible.
- Usage of C++11 `virtual`, `override`, `final` keywords: Please follow the
`C++ Core Guideline C.128 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rh-override>`_.
That means, you should only use `virtual` to declare a new virtual
function, `override` to indicate you are overriding an existing virtual
function, and `final` to prevent any further overriding.
- Trivial destructors: Prefer not writing destructors when they are empty and `default`.
.. code-block:: c++
// don't write destructors for A or B like this
class A : protected Pointers {
public:
A();
~A() override {}
};
class B : protected Pointers {
public:
B();
~B() override = default;
};
// instead, let the compiler create the implicit default destructor by not writing it
class A : protected Pointers {
public:
A();
};
class B : protected Pointers {
public:
B();
};
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not** contain
any ``using`` statements. Typically that would be only the header for

6
doc/src/Packages_details.rst
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@ -1880,6 +1880,12 @@ MPIIO library. It adds :doc:`dump styles <dump>` with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
**Install:**
The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.

4
doc/src/Run_output.rst
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@ -106,7 +106,7 @@ individual ranks. Here is an example output for this section:
----------
The third section above lists the number of owned atoms (Nlocal),
ghost atoms (Nghost), and pair-wise neighbors stored per processor.
ghost atoms (Nghost), and pairwise neighbors stored per processor.
The max and min values give the spread of these values across
processors with a 10-bin histogram showing the distribution. The total
number of histogram counts is equal to the number of processors.
@ -114,7 +114,7 @@ number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pair-wise neighbors and special neighbors that LAMMPS keeps track
for pairwise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
of times neighbor lists were rebuilt is tallied, as is the number of
potentially *dangerous* rebuilds. If atom movement triggered neighbor

2
doc/src/Speed_kokkos.rst
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@ -214,7 +214,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
The default for the :doc:`package kokkos <package>` command when
running on KNL is to use "half" neighbor lists and set the Newton flag
to "on" for both pairwise and bonded interactions. This will typically
be best for many-body potentials. For simpler pair-wise potentials, it
be best for many-body potentials. For simpler pairwise potentials, it
may be faster to use a "full" neighbor list with Newton flag to "off".
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
the default :doc:`package kokkos <package>` options. See its page for

38
doc/src/angle_class2.rst
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@ -64,34 +64,44 @@ These are the 4 coefficients for the :math:`E_a` formula:
radians internally; hence the various :math:`K` are effectively energy
per radian\^2 or radian\^3 or radian\^4.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 4 coefficients, the
first of which is "bb" to indicate they are BondBond coefficients. In
a data file, these coefficients should be listed under a "BondBond
Coeffs" heading and you must leave out the "bb", i.e. only list 3
coefficients after the angle type.
* bb
* :math:`M` (energy/distance\^2)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff <angle_coeff>`
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 5 coefficients, the
first of which is "ba" to indicate they are BondAngle coefficients.
In a data file, these coefficients should be listed under a "BondAngle
Coeffs" heading and you must leave out the "ba", i.e. only list 4
coefficients after the angle type.
* ba
* :math:`N_1` (energy/distance\^2)
* :math:`N_2` (energy/distance\^2)
* :math:`N_1` (energy/distance)
* :math:`N_2` (energy/distance)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
.. note::
It is important that the order of the I,J,K atoms in each angle
listed in the Angles section of the data file read by the
:doc:`read_data <read_data>` command be consistent with the order
of the :math:`r_1` and :math:`r_2` BondBond and BondAngle
coefficients. This is because the terms in the formulas for
:math:`E_{bb}` and :math:`E_{ba}` will use the I,J atoms to compute
:math:`r_{ij}` and the J,K atoms to compute :math:`r_{jk}`.
----------
.. include:: accel_styles.rst

2
doc/src/balance.rst
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@ -383,7 +383,7 @@ multiple groups, its weight is the product of the weight factors.
This weight style is useful in combination with pair style
:doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
potential with a fast pair-wise potential. It is also useful when
potential with a fast pairwise potential. It is also useful when
using :doc:`run_style respa <run_style>` where some portions of the
system have many bonded interactions and others none. It assumes that
the computational cost for each group remains constant over time.

1
doc/src/compute.rst
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@ -174,6 +174,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`angle <compute_angle>` - energy of each angle sub-style
* :doc:`angle/local <compute_angle_local>` - theta and energy of each angle
* :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
* :doc:`ave/sphere/atom <compute_ave_sphere_atom>` - compute local density and temperature around each atom
* :doc:`basal/atom <compute_basal_atom>` - calculates the hexagonal close-packed "c" lattice vector of each atom
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
* :doc:`bond <compute_bond>` - energy of each bond sub-style

101
doc/src/compute_ave_sphere_atom.rst Normal file
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@ -0,0 +1,101 @@
.. index:: compute ave/sphere/atom
.. index:: compute ave/sphere/atom/kk
compute ave/sphere/atom command
================================
Accelerator Variants: *ave/sphere/atom/kk*
Syntax
""""""
.. parsed-literal::
compute ID group-ID ave/sphere/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* ave/sphere/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all ave/sphere/atom
compute 1 all ave/sphere/atom cutoff 5.0
comm_modify cutoff 5.0
Description
"""""""""""
Define a computation that calculates the local density and temperature
for each atom and neighbors inside a spherical cutoff.
The optional keyword *cutoff* defines the distance cutoff
used when searching for neighbors. The default value is the cutoff
specified by the pair style. If no pair style is defined, then a cutoff
must be defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is defined),
the *comm_modify cutoff* option must also be set to match that of the
*cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the :doc:`special_bonds <special_bonds>`
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
:doc:`rerun <rerun>` command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
:doc:`special_bonds <special_bonds>` command that includes all pairs in
the neighbor list.
----------
.. include:: accel_styles.rst
----------
Output info
"""""""""""
This compute calculates a per-atom array with two columns: density and temperature.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff

21
doc/src/compute_heat_flux.rst
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@ -89,13 +89,20 @@ included in the calculation.
.. warning::
The compute *heat/flux* has been reported to produce unphysical
values for angle, dihedral and improper contributions
values for angle, dihedral, improper and constraint force contributions
when used with :doc:`compute stress/atom <compute_stress_atom>`,
as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
You are strongly advised to
as discussed in :ref:`(Surblys2019) <Surblys3>`, :ref:`(Boone) <Boone>`
and :ref:`(Surblys2021) <Surblys4>`. You are strongly advised to
use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
which has been implemented specifically for such cases.
.. warning::
Due to an implementation detail, the :math:`y` and :math:`z`
components of heat flux from :doc:`fix rigid <fix_rigid>`
contribution when computed via :doc:`compute stress/atom <compute_stress_atom>`
are highly unphysical and should not be used.
The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux :math:`\mathbf{J}`
to the thermal conductivity :math:`\kappa`:
@ -232,10 +239,14 @@ none
----------
.. _Surblys2:
.. _Surblys3:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _Boone:
**(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
.. _Surblys4:
**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).

2
doc/src/compute_pressure.rst
View File

@ -141,7 +141,7 @@ Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
:doc:`thermo_style <thermo_style>`,
:doc:`thermo_style <thermo_style>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
Default
"""""""

2
doc/src/compute_pressure_cylinder.rst
View File

@ -61,7 +61,7 @@ Restrictions
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pair-wise force
due to exclusions for special bonds) and requires pairwise force
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included

45
doc/src/compute_stress_atom.rst
View File

@ -87,6 +87,10 @@ Tersoff 3-body interaction) is assigned in equal portions to each atom
in the set. E.g. 1/4 of the dihedral virial to each of the 4 atoms,
or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
a water molecule via the :doc:`fix shake <fix_shake>` command.
As an exception, the virial contribution from
constraint forces in :doc:`fix rigid <fix_rigid>` on each atom
is computed from the constraint force acting on the corresponding atom
and its position, i.e. the total virial is not equally distributed.
In case of compute *centroid/stress/atom*, the virial contribution is:
@ -103,13 +107,25 @@ atom :math:`I` due to the interaction and the relative position
:math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
of the interacting atoms, i.e. centroid, is used. As the geometric
center is different for each interaction, the :math:`\mathbf{r}_{I0}`
also differs. The sixth and seventh terms, Kspace and :doc:`fix
<fix>` contribution respectively, are computed identical to compute
*stress/atom*. Although the total system virial is the same as
also differs. The sixth term, Kspace contribution,
is computed identically to compute *stress/atom*.
The seventh term is handed differently depending on
if the constraint forces are due to :doc:`fix shake <fix_shake>`
or :doc:`fix rigid <fix_rigid>`.
In case of SHAKE constraints, each distance constraint is
handed as a pairwise interaction.
E.g. in case of a water molecule, two OH and one HH distance
constraints are treated as three pairwise interactions.
In case of :doc:`fix rigid <fix_rigid>`,
all constraint forces in the molecule are treated
as a single many-body interaction with a single centroid position.
In case of water molecule, the formula expression would become
identical to that of the three-body angle interaction.
Although the total system virial is the same as
compute *stress/atom*, compute *centroid/stress/atom* is know to
result in more consistent heat flux values for angle, dihedrals and
improper contributions when computed via :doc:`compute heat/flux
<compute_heat_flux>`.
result in more consistent heat flux values for angle, dihedrals,
improper and constraint force contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution all of the
virial contribution terms are included in the per-atom stress tensor.
@ -134,7 +150,8 @@ contribution for the cluster interaction is divided evenly among those
atoms.
Details of how compute *centroid/stress/atom* obtains the virial for
individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
individual atoms are given in :ref:`(Surblys2019) <Surblys1>` and
:ref:`(Surblys2021) <Surblys2>`, where the
idea is that the virial of the atom :math:`I` is the result of only
the force :math:`\mathbf{F}_I` on the atom due to the interaction and
its positional vector :math:`\mathbf{r}_{I0}`, relative to the
@ -235,10 +252,10 @@ between the pair of particles. All bond styles are supported. All
angle, dihedral, improper styles are supported with the exception of
INTEL and KOKKOS variants of specific styles. It also does not
support models with long-range Coulombic or dispersion forces,
i.e. the kspace_style command in LAMMPS. It also does not support the
following fixes which add rigid-body constraints: :doc:`fix shake
<fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
i.e. the kspace_style command in LAMMPS. It also does not implement the
following fixes which add rigid-body constraints:
:doc:`fix rigid/* <fix_rigid>` and the OpenMP accelerated version of :doc:`fix rigid/small <fix_rigid>`,
while all other :doc:`fix rigid/*/small <fix_rigid>` are implemented.
LAMMPS will generate an error if one of these options is included in
your model. Extension of centroid stress calculations to these force
@ -270,4 +287,8 @@ none
.. _Surblys1:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _Surblys2:
**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).

90
doc/src/dump.rst
View File

@ -137,7 +137,7 @@ Examples
dump myDump all atom/gz 100 dump.atom.gz
dump myDump all atom/zstd 100 dump.atom.zst
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 2 subgroup atom/mpiio 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
@ -169,11 +169,12 @@ or multiple smaller files).
.. note::
Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
written to a dump file may be slightly outside the simulation box.
Re-neighbor timesteps will not typically coincide with the timesteps
dump snapshots are written. See the :doc:`dump_modify pbc <dump_modify>` command if you with to force coordinates to be
Because periodic boundary conditions are enforced only on timesteps
when neighbor lists are rebuilt, the coordinates of an atom written
to a dump file may be slightly outside the simulation box.
Re-neighbor timesteps will not typically coincide with the
timesteps dump snapshots are written. See the :doc:`dump_modify
pbc <dump_modify>` command if you with to force coordinates to be
strictly inside the simulation box.
.. note::
@ -189,20 +190,21 @@ or multiple smaller files).
multiple processors, each of which owns a subset of the atoms.
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by
atom ID is on by default. See the :doc:`dump_modify <dump_modify>` doc
page for details.
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting
by atom ID is on by default. See the :doc:`dump_modify <dump_modify>`
doc page for details.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles are identical
in command syntax to the corresponding styles without "gz", however,
they generate compressed files using the zlib library. Thus the filename
suffix ".gz" is mandatory. This is an alternative approach to writing
compressed files via a pipe, as done by the regular dump styles, which
may be required on clusters where the interface to the high-speed network
disallows using the fork() library call (which is needed for a pipe).
For the remainder of this doc page, you should thus consider the *atom*
and *atom/gz* styles (etc) to be inter-changeable, with the exception
of the required filename suffix.
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
are identical in command syntax to the corresponding styles without
"gz", however, they generate compressed files using the zlib
library. Thus the filename suffix ".gz" is mandatory. This is an
alternative approach to writing compressed files via a pipe, as done
by the regular dump styles, which may be required on clusters where
the interface to the high-speed network disallows using the fork()
library call (which is needed for a pipe). For the remainder of this
doc page, you should thus consider the *atom* and *atom/gz* styles
(etc) to be inter-changeable, with the exception of the required
filename suffix.
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
@ -219,6 +221,11 @@ you should thus consider the *atom* and *atom/mpiio* styles (etc) to
be inter-changeable. The one exception is how the filename is
specified for the MPI-IO styles, as explained below.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
The precision of values output to text-based dump files can be
controlled by the :doc:`dump_modify format <dump_modify>` command and
its options.
@ -275,10 +282,11 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they represent a bounding box. See the :doc:`Howto triclinic <Howto_triclinic>` page for a geometric description
of triclinic boxes, as defined by LAMMPS, simple formulas for how the
6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from
the triclinic parameters, and how to transform those parameters to and
of xlo, etc, since they represent a bounding box. See the :doc:`Howto
triclinic <Howto_triclinic>` page for a geometric description of
triclinic boxes, as defined by LAMMPS, simple formulas for how the 6
bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the
triclinic parameters, and how to transform those parameters to and
from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
@ -310,23 +318,24 @@ written to the dump file. This local data is typically calculated by
each processor based on the atoms it owns, but there may be zero or
more entities per atom, e.g. a list of bond distances. An explanation
of the possible dump local attributes is given below. Note that by
using input from the :doc:`compute property/local <compute_property_local>` command with dump local,
it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
:doc:`read_data <read_data>` command.
using input from the :doc:`compute property/local
<compute_property_local>` command with dump local, it is possible to
generate information on bonds, angles, etc that can be cut and pasted
directly into a data file read by the :doc:`read_data <read_data>`
command.
Style *cfg* has the same command syntax as style *custom* and writes
extended CFG format files, as used by the
`AtomEye <http://li.mit.edu/Archive/Graphics/A/>`_ visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wildcard "\*" must be included in the filename, as
discussed below. The list of atom attributes for style *cfg* must
begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
since these quantities are needed to write the CFG files in the
appropriate format (though the "mass" and "type" fields do not appear
explicitly in the file). Any remaining attributes will be stored as
"auxiliary properties" in the CFG files. Note that you will typically
want to use the :doc:`dump_modify element <dump_modify>` command with
extended CFG format files, as used by the `AtomEye
<http://li.mit.edu/Archive/Graphics/A/>`_ visualization package.
Since the extended CFG format uses a single snapshot of the system per
file, a wildcard "\*" must be included in the filename, as discussed
below. The list of atom attributes for style *cfg* must begin with
either "mass type xs ys zs" or "mass type xsu ysu zsu" since these
quantities are needed to write the CFG files in the appropriate format
(though the "mass" and "type" fields do not appear explicitly in the
file). Any remaining attributes will be stored as "auxiliary
properties" in the CFG files. Note that you will typically want to
use the :doc:`dump_modify element <dump_modify>` command with
CFG-formatted files, to associate element names with atom types, so
that AtomEye can render atoms appropriately. When unwrapped
coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye
@ -452,6 +461,11 @@ use the :doc:`read_dump <read_dump>` command or perform other
post-processing, just as if the dump file was not written using
MPI-IO.
.. warning::
The MPIIO package is currently unmaintained and has become
unreliable. Use with caution.
Note that MPI-IO dump files are one large file which all processors
write to. You thus cannot use the "%" wildcard character described
above in the filename since that specifies generation of multiple

165
doc/src/dump_modify.rst
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@ -17,13 +17,14 @@ Syntax
* one or more keyword/value pairs may be appended
* these keywords apply to various dump styles
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
.. parsed-literal::
*append* arg = *yes* or *no*
*at* arg = N
N = index of frame written upon first dump
*balance* arg = *yes* or *no*
*buffer* arg = *yes* or *no*
*delay* arg = Dstep
Dstep = delay output until this timestep
@ -32,6 +33,9 @@ Syntax
*every* arg = N
N = dump every this many timesteps
N can be a variable (see below)
*every/time* arg = Delta
Delta = dump every this interval in simulation time (time units)
Delta can be a variable (see below)
*fileper* arg = Np
Np = write one file for every this many processors
*first* arg = *yes* or *no*
@ -197,11 +201,19 @@ will be accepted.
----------
The *every* keyword changes the dump frequency originally specified by
the :doc:`dump <dump>` command to a new value. The every keyword can be
specified in one of two ways. It can be a numeric value in which case
it must be > 0. Or it can be an :doc:`equal-style variable <variable>`,
which should be specified as v_name, where name is the variable name.
The *every* keyword can be used with any dump style except the *dcd*
and *xtc* styles. It does two things. It specifies that the interval
between dump snapshots will be set in timesteps, which is the default
if the *every* or *every/time* keywords are not used. See the
*every/time* keyword for how to specify the interval in simulation
time, i.e. in time units of the :doc:`units <units>` command. The
*every* keyword also sets the interval value, which overrides the dump
frequency originally specified by the :doc:`dump <dump>` command.
The *every* keyword can be specified in one of two ways. It can be a
numeric value in which case it must be > 0. Or it can be an
:doc:`equal-style variable <variable>`, which should be specified as
v_name, where name is the variable name.
In this case, the variable is evaluated at the beginning of a run to
determine the next timestep at which a dump snapshot will be written
@ -210,11 +222,12 @@ determine the next timestep, etc. Thus the variable should return
timestep values. See the stagger() and logfreq() and stride() math
functions for :doc:`equal-style variables <variable>`, as examples of
useful functions to use in this context. Other similar math functions
could easily be added as options for :doc:`equal-style variables <variable>`. Also see the next() function, which allows
use of a file-style variable which reads successive values from a
file, each time the variable is evaluated. Used with the *every*
keyword, if the file contains a list of ascending timesteps, you can
output snapshots whenever you wish.
could easily be added as options for :doc:`equal-style variables
<variable>`. Also see the next() function, which allows use of a
file-style variable which reads successive values from a file, each
time the variable is evaluated. Used with the *every* keyword, if the
file contains a list of ascending timesteps, you can output snapshots
whenever you wish.
Note that when using the variable option with the *every* keyword, you
need to use the *first* option if you want an initial snapshot written
@ -255,14 +268,103 @@ in file tmp.times:
----------
The *every/time* keyword can be used with any dump style except the
*dcd* and *xtc* styles. It does two things. It specifies that the
interval between dump snapshots will be set in simulation time,
i.e. in time units of the :doc:`units <units>` command. This can be
useful when the timestep size varies during a simulation run, e.g. by
use of the :doc:`fix dt/reset <fix_dt_reset>` command. The default is
to specify the interval in timesteps; see the *every* keyword. The
*every/time* command also sets the interval value.
.. note::
If you wish dump styles *atom*, *custom*, *local*, or *xyz* to
include the simulation time as a field in the header portion of
each snapshot, you also need to use the dump_modify *time* keyword
with a setting of *yes*. See its documentation below.
Note that since snapshots are output on simulation steps, each
snapshot will be written on the first timestep whose associated
simulation time is >= the exact snapshot time value.
As with the *every* option, the *Delta* value can be specified in one
of two ways. It can be a numeric value in which case it must be >
0.0. Or it can be an :doc:`equal-style variable <variable>`, which
should be specified as v_name, where name is the variable name.
In this case, the variable is evaluated at the beginning of a run to
determine the next simulation time at which a dump snapshot will be
written out. On that timestep the variable will be evaluated again to
determine the next simulation time, etc. Thus the variable should
return values in time units. Note the current timestep or simulation
time can be used in an :doc:`equal-style variables <variable>` since
they are both thermodynamic keywords. Also see the next() function,
which allows use of a file-style variable which reads successive
values from a file, each time the variable is evaluated. Used with
the *every/time* keyword, if the file contains a list of ascending
simulation times, you can output snapshots whenever you wish.
Note that when using the variable option with the *every/time*
keyword, you need to use the *first* option if you want an initial
snapshot written to the dump file. The *every/time* keyword cannot be
used with the dump *dcd* style.
For example, the following commands will write snapshots at successive
simulation times which grow by a factor of 1.5 with each interval.
The dt value used in the variable is to avoid a zero result when the
initial simulation time is 0.0.
.. code-block:: LAMMPS
variable increase equal 1.5*(time+dt)
dump 1 all atom 100 tmp.dump
dump_modify 1 every/time v_increase first yes
The following commands would write snapshots at the times listed in
file tmp.times:
.. code-block:: LAMMPS
variable f file tmp.times
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every/time v_s
.. note::
When using a file-style variable with the *every/time* keyword, the
file of timesteps must list a first time that is beyond the time
associated with the current timestep (e.g. it cannot be 0.0). And
it must list one or more times beyond the length of the run you
perform. This is because the dump command will generate an error
if the next time it reads from the file is not a value greater than
the current time. Thus if you wanted output at times 0,15,100 of a
run of length 100 in simulation time, the file should contain the
values 15,100,101 and you should also use the dump_modify first
command. Any final value > 100 could be used in place of 101.
----------
The *first* keyword determines whether a dump snapshot is written on
the very first timestep after the dump command is invoked. This will
always occur if the current timestep is a multiple of N, the frequency
specified in the :doc:`dump <dump>` command, including timestep 0. But
if this is not the case, a dump snapshot will only be written if the
setting of this keyword is *yes*\ . If it is *no*, which is the
always occur if the current timestep is a multiple of $N$, the
frequency specified in the :doc:`dump <dump>` command or
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
It will also always occur if the current simulation time is a multiple
of *Delta*, the time interval specified in the doc:`dump_modify
every/time <dump_modify>` command.
But if this is not the case, a dump snapshot will only be written if
the setting of this keyword is *yes*\ . If it is *no*, which is the
default, then it will not be written.
Note that if the argument to the :doc:`dump_modify every
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
a variable and not a numeric value, then specifying *first yes* is the
only way to write a dump snapshot on the first timestep after the dump
command is invoked.
----------
The *flush* keyword determines whether a flush operation is invoked
@ -342,10 +444,10 @@ The *fileper* keyword is documented below with the *nfile* keyword.
----------
The *header* keyword toggles whether the dump file will include a header.
Excluding a header will reduce the size of the dump file for fixes such as
:doc:`fix pair/tracker <fix_pair_tracker>` which do not require the information
typically written to the header.
The *header* keyword toggles whether the dump file will include a
header. Excluding a header will reduce the size of the dump file for
fixes such as :doc:`fix pair/tracker <fix_pair_tracker>` which do not
require the information typically written to the header.
----------
@ -561,9 +663,19 @@ The dump *local* style cannot be sorted by atom ID, since there are
typically multiple lines of output per atom. Some dump styles, such
as *dcd* and *xtc*, require sorting by atom ID to format the output
file correctly. If multiple processors are writing the dump file, via
the "%" wildcard in the dump filename, then sorting cannot be
the "%" wildcard in the dump filename and the *nfile* or *fileper*
keywords are set to non-default values (i.e. the number of dump file
pieces is not equal to the number of procs), then sorting cannot be
performed.
In a parallel run, the per-processor dump file pieces can have
significant imbalance in number of lines of per-atom info. The *balance*
keyword determines whether the number of lines in each processor
snapshot are balanced to be nearly the same. A balance value of *no*
means no balancing will be done, while *yes* means balancing will be
performed. This balancing preserves dump sorting order. For a serial
run, this option is ignored since the output is already balanced.
.. note::
Unless it is required by the dump style, sorting dump file
@ -639,16 +751,20 @@ threshold criterion is met. Otherwise it is not met.
----------
The *time* keyword only applies to the dump *atom*, *custom*, and
*local* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). If set to *yes*, each frame will will
contain two extra lines before the "ITEM: TIMESTEP" entry:
The *time* keyword only applies to the dump *atom*, *custom*, *local*,
and *xyz* styles (and their COMPRESS package versions *atom/gz*,
*custom/gz* and *local/gz*\ ). For the first 3 styles, if set to
*yes*, each frame will will contain two extra lines before the "ITEM:
TIMESTEP" entry:
.. parsed-literal::
ITEM: TIME
\<elapsed time\>
For the *xyz* style, the simulation time is included on the same line
as the timestep value.
This will output the current elapsed simulation time in current
time units equivalent to the :doc:`thermo keyword <thermo_style>` *time*\ .
This is to simplify post-processing of trajectories using a variable time
@ -725,6 +841,7 @@ Default
The option defaults are
* append = no
* balance = no
* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz*
* element = "C" for every atom type
* every = whatever it was set to via the :doc:`dump <dump>` command

9
doc/src/dynamical_matrix.rst
View File

@ -1,8 +1,11 @@
.. index:: dynamical_matrix
.. index:: dynamical_matrix/kk
dynamical_matrix command
========================
Accelerator Variants: dynamical_matrix/kk
Syntax
""""""
@ -56,6 +59,12 @@ If the style eskm is selected, the dynamical matrix will be in units of
inverse squared femtoseconds. These units will then conveniently leave
frequencies in THz.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

3
doc/src/fix.rst
View File

@ -271,7 +271,8 @@ accelerated styles exist.
* :doc:`npt/eff <fix_nh_eff>` - NPT for nuclei and electrons in the electron force field model
* :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
* :doc:`npt/uef <fix_nh_uef>` - NPT style time integration with diagonal flow
* :doc:`numdiff <fix_numdiff>` - compute derivatives of per-atom data from finite differences
* :doc:`numdiff <fix_numdiff>` - numerically approximate atomic forces using finite energy differences
* :doc:`numdiff/virial <fix_numdiff_virial>` - numerically approximate virial stress tensor using finite energy differences
* :doc:`nve <fix_nve>` - constant NVE time integration
* :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` - NVE for aspherical particles without forces

75
doc/src/fix_charge_regulation.rst
View File

@ -20,13 +20,13 @@ Syntax
.. parsed-literal::
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *rxd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
*pH* value = pH of the solution (can be specified as an equal-style variable)
*pKa* value = acid dissociation constant
*pKb* value = base dissociation constant
*pIp* value = chemical potential of free cations
*pIm* value = chemical potential of free anions
*pKs* value = solution self-dissociation constant
*pKa* value = acid dissociation constant (in the -log10 representation)
*pKb* value = base dissociation constant (in the -log10 representation)
*pIp* value = activity (effective concentration) of free cations (in the -log10 representation)
*pIm* value = activity (effective concentration) of free anions (in the -log10 representation)
*pKs* value = solvent self-dissociation constant (in the -log10 representation)
*acid_type* = atom type of acid groups
*base_type* = atom type of base groups
*lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
@ -34,7 +34,7 @@ Syntax
*tempfixid* value = fix ID of temperature thermostat
*nevery* value = invoke this fix every nevery steps
*nmc* value = number of charge regulation MC moves to attempt every nevery steps
*xrd* value = cutoff distance for acid/base reaction
*rxd* value = cutoff distance for acid/base reaction
*seed* value = random # seed (positive integer)
*tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
*group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
@ -47,7 +47,7 @@ Examples
""""""""
.. code-block:: LAMMPS
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT
fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
@ -92,7 +92,11 @@ where the fix attempts to charge :math:`\mathrm{A}` (discharge
:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
insert (delete) a proton (atom type 2). Besides, the fix implements
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly
\mathrm{H}^++\mathrm{OH}^-`.
However, this approach is highly
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
both protons and hydroxyl ions is low, resulting in a relatively low
acceptance rate of MC moves.
@ -102,24 +106,31 @@ reactions, which can be easily achieved via
.. code-block:: LAMMPS
fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
where particles of atom type 4 and 5 are the salt cations and anions,
both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) <Curk1>` and
:ref:`(Landsgesell) <Landsgesell>` for more details.
Similarly, we could have simultaneously added a base ionization reaction
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
.. code-block:: LAMMPS
fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
fix acid_base_reaction all charge/regulation 2 3 acid_type 1 base_type 6 pH 7.0 pKa 5.0 pKb 6.0 pIp 7.0 pIm 7.0
where the fix will attempt to charge :math:`\mathrm{B}` (discharge
:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If
neither the acid or the base type is specified, for example,
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.
Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) <Curk1>`. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read,
.. code-block:: LAMMPS
fix acid_reaction_combined all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 5.958 pIm 5.958
If neither the acid or the base type is specified, for example,
.. code-block:: LAMMPS
@ -127,11 +138,11 @@ neither the acid or the base type is specified, for example,
the fix simply inserts or deletes an ion pair of a free cation (atom
type 4) and a free anion (atom type 5) as done in a conventional
grand-canonical MC simulation.
grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword.
The fix is compatible with LAMMPS sub-packages such as *molecule* or
*rigid*. That said, the acid and base particles can be part of larger
*rigid*. The acid and base particles can be part of larger
molecules or rigid bodies. Free ions that are inserted to or deleted
from the system must be defined as single particles (no bonded
interactions allowed) and cannot be part of larger molecules or rigid
@ -153,14 +164,14 @@ Langevin thermostat:
fix fT all langevin 1.0 1.0 1.0 123
fix_modify fT temp dtemp
The chemical potential units (e.g. pH) are in the standard log10
The units of pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10
representation assuming reference concentration :math:`\rho_0 =
\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit
conversion, the length (in nanometers) of the LAMMPS unit length must be
specified via *lunit_nm* (default is set to the Bjerrum length in water
at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
ideal solution limit, the concentration of free ions will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
\mathrm{mol}/\mathrm{l}`. For example, in the dilute
ideal solution limit, the concentration of free cations will be
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit
conversion, the the value of the LAMMPS unit length must be
specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water
at room temperature (0.71 nm), *lunit_nm* = 0.71.
The temperature used in MC acceptance probability is set by *temp*. This
temperature should be the same as the temperature set by the molecular
@ -171,10 +182,10 @@ thermostat fix-ID is *fT*. The inserted particles attain a random
velocity corresponding to the specified temperature. Using *tempfixid*
overrides any fixed temperature set by *temp*.
The *xrd* keyword can be used to restrict the inserted/deleted
The *rxd* keyword can be used to restrict the inserted/deleted
counterions to a specific radial distance from an acid or base particle
that is currently participating in a reaction. This can be used to
simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
simulate more realist reaction dynamics. If *rxd* = 0 or *rxd* > *L* /
2, where *L* is the smallest box dimension, the radial restriction is
automatically turned off and free ion can be inserted or deleted
anywhere in the simulation box.
@ -258,18 +269,18 @@ Default
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
100; nmc = 100; rxd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
[1/3, 1/3, 1/3], group-ID = all
----------
.. _Curk1:
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Accelerated simulation method for charge regulation effects", JCP 156 (2022).
.. _Curk2:
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL 126 (2021)
.. _Landsgesell:

18
doc/src/fix_dt_reset.rst
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@ -78,13 +78,20 @@ outer loop (largest) timestep, which is the same timestep that the
Note that the cumulative simulation time (in time units), which
accounts for changes in the timestep size as a simulation proceeds,
can be accessed by the :doc:`thermo_style time <thermo_style>` keyword.
can be accessed by the :doc:`thermo_style time <thermo_style>`
keyword.
Also note that the :doc:`dump_modify every/time <dump_modify>` option
allows dump files to be written at intervals specified by simulation
time, rather than by timesteps. Simulation time is in time units;
see the :doc:`units <units>` doc page for details.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar stores the last
@ -93,7 +100,8 @@ timestep on which the timestep was reset to a new value.
The scalar value calculated by this fix is "intensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -102,7 +110,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`timestep <timestep>`
:doc:`timestep <timestep>`, :doc:`dump_modify every/time <dump_modify>`
Default
"""""""

23
doc/src/fix_numdiff.rst
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@ -13,16 +13,15 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* numdiff = style name of this fix command
* Nevery = calculate force by finite difference every this many timesteps
* delta = finite difference displacement length (distance units)
* delta = size of atom displacements (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all numdiff 1 0.0001
fix 1 all numdiff 10 1e-6
fix 1 all numdiff 100 0.01
fix 1 movegroup numdiff 100 0.01
Description
"""""""""""
@ -67,16 +66,17 @@ by two times *delta*.
The cost of each energy evaluation is essentially the cost of an MD
timestep. Thus invoking this fix once for a 3d system has a cost
of 6N timesteps, where N is the total number of atoms in the system
(assuming all atoms are included in the group). So this fix can be
very expensive to use for large systems.
of 6N timesteps, where N is the total number of atoms in the system.
So this fix can be very expensive to use for large systems.
One expedient alternative is to define the fix for a group containing
only a few atoms.
----------
The *Nevery* argument specifies on what timesteps the force will
be used calculated by finite difference.
The *delta* argument specifies the positional displacement each
The *delta* argument specifies the size of the displacement each
atom will undergo.
----------
@ -93,7 +93,12 @@ This fix produces a per-atom array which can be accessed by various
the force on each atom as calculated by finite difference. The
per-atom values can only be accessed on timesteps that are multiples
of *Nevery* since that is when the finite difference forces are
calculated.
calculated. See the examples in *examples/numdiff* directory
to see how this fix can be used to directly compare with
the analytic forces computed by LAMMPS.
The array values calculated by this compute
will be in force :doc:`units <units>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
@ -108,7 +113,7 @@ was built with that package. See the :doc:`Build package <Build_package>` page
Related commands
""""""""""""""""
:doc:`dynamical_matrix <dynamical_matrix>`,
:doc:`dynamical_matrix <dynamical_matrix>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
Default
"""""""

115
doc/src/fix_numdiff_virial.rst Normal file
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@ -0,0 +1,115 @@
.. index:: fix numdiff/virial
fix numdiff/virial command
==========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID numdiff/virial Nevery delta
* ID, group-ID are documented in :doc:`fix <fix>` command
* numdiff/virial = style name of this fix command
* Nevery = calculate virial by finite difference every this many timesteps
* delta = magnitude of strain fields (dimensionless)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all numdiff/stress 10 1e-6
Description
"""""""""""
Calculate the virial stress tensor through a finite difference calculation of
energy versus strain. These values can be compared to the analytic virial
tensor computed by pair styles, bond styles, etc. This can be useful for
debugging or other purposes. The specified group must be "all".
This fix applies linear strain fields of magnitude *delta* to all the
atoms relative to a point at the center of the box. The
strain fields are in six different directions, corresponding to the
six Cartesian components of the stress tensor defined by LAMMPS.
For each direction it applies the strain field in both the positive
and negative senses, and the new energy of the entire system
is calculated after each. The difference in these two energies
divided by two times *delta*, approximates the corresponding
component of the virial stress tensor, after applying
a suitable unit conversion.
.. note::
It is important to choose a suitable value for delta, the magnitude of
strains that are used to generate finite difference
approximations to the exact virial stress. For typical systems, a value in
the range of 1 part in 1e5 to 1e6 will be sufficient.
However, the best value will depend on a multitude of factors
including the stiffness of the interatomic potential, the thermodynamic
state of the material being probed, and so on. The only way to be sure
that you have made a good choice is to do a sensitivity study on a
representative atomic configuration, sweeping over a wide range of
values of delta. If delta is too small, the output values will vary
erratically due to truncation effects. If delta is increased beyond a
certain point, the output values will start to vary smoothly with
delta, due to growing contributions from higher order derivatives. In
between these two limits, the numerical virial values should be largely
independent of delta.
----------
The *Nevery* argument specifies on what timesteps the force will
be used calculated by finite difference.
The *delta* argument specifies the size of the displacement each
atom will undergo.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix produces a global vector which can be accessed by various
:doc:`output commands <Howto_output>`, which stores the components of
the virial stress tensor as calculated by finite difference. The
global vector can only be accessed on timesteps that are multiples
of *Nevery* since that is when the finite difference virial is
calculated. See the examples in *examples/numdiff* directory
to see how this fix can be used to directly compare with
the analytic virial stress tensor computed by LAMMPS.
The order of the virial stress tensor components is *xx*, *yy*, *zz*,
*yz*, *xz*, and *xy*, consistent with Voigt notation. Note that
the vector produced by :doc:`compute pressure <compute_pressure>`
uses a different ordering, with *yz* and *xy* swapped.
The vector values calculated by this compute are
"intensive". The vector values will be in pressure
:doc:`units <units>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix numdiff <fix_numdiff>`, :doc:`compute pressure <compute_pressure>`
Default
"""""""
none

9
doc/src/fix_nvt_sllod.rst
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@ -66,7 +66,10 @@ 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
<Daivis>`.
The LAMMPS implementation corresponds to the p-SLLOD variant
of SLLOD. :ref:`(Edwards) <Edwards>`.
The equations of motion 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.
@ -180,6 +183,10 @@ Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
.. _Edwards:
**(Edwards)** Edwards, Baig, and Keffer, J Chem Phys 124, 194104 (2006).
.. _Daivis-sllod:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),

9
doc/src/fix_viscosity.rst
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@ -108,10 +108,11 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper <Muller-Plathe2>
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described on the :doc:`Howto nemd <Howto_nemd>` doc page.
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command. Thus they cannot be run on a charged
system using a :doc:`PPPM solver <kspace_style>` since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the
box orthogonal; thus it does not suffer from this limitation.
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command.
Some features or combination of settings in LAMMPS do not support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
thus it does not suffer from these limitations.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

2
doc/src/package.rst
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@ -460,7 +460,7 @@ using *neigh/thread* *on*, a full neighbor list must also be used. Using
is turned on by default only when there are 16K atoms or less owned by
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
potentials support this keyword yet, and only thread over atoms. Many
simple pair-wise potentials such as Lennard-Jones do support threading
simple pairwise potentials such as Lennard-Jones do support threading
over both atoms and neighbors.
The *newton* keyword sets the Newton flags for pairwise and bonded

2
doc/src/pair_charmm.rst
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@ -119,7 +119,7 @@ name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
shown in the formula below as S(r)), which ramps the energy smoothly
to zero between the inner and outer cutoff. This can cause
irregularities in pair-wise forces (due to the discontinuous second
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.

2
doc/src/pair_dpd.rst
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@ -50,7 +50,7 @@ Style *dpd* computes a force field for dissipative particle dynamics
Style *dpd/tstat* invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This pair-wise thermostat can be used in conjunction with any
field. This pairwise thermostat can be used in conjunction with any
:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use

90
doc/src/pair_harmonic_cut.rst Normal file
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@ -0,0 +1,90 @@
.. index:: pair_style harmonic/cut
.. index:: pair_style harmonic/cut/omp
pair_style harmonic/cut command
===============================
Accelerator Variants: *harmonic/cut/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
* style = *harmonic/cut*
Examples
""""""""
.. code-block:: LAMMPS
pair_style harmonic/cut 2.5
pair_coeff * * 0.2 2.0
pair_coeff 1 1 0.5 2.5
Description
"""""""""""
Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with the formula
.. math::
E = k (r_c - r)^2 \qquad r < r_c
:math:`r_c` is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`k` (energy units)
* :math:`r_c` (distance units)
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the :math:`k` and :math:`r_c`
coefficients can be mixed. The default mix value is *geometric*.
See the "pair_modify" command for details.
Since the potential is zero at and beyond the cutoff parameter by
construction, there is no need to support support the :doc:`pair_modify
<pair_modify>` shift or tail options for the energy and pressure of the
pair interaction.
These pair styles write their information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands do not need to be specified in an input script
that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
The *harmonic/cut* pair style is only enabled if LAMMPS was
built with the EXTRA-PAIR package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none

3
doc/src/pair_nm.rst
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@ -195,5 +195,4 @@ none
.. _Dietz:
**(Dietz)** J.D. Dietz, R.S. Hoy, "Facile equilibration of well-entangled
semi-flexible bead-spring polymer melts" arXiv:2109.11001
**(Dietz)** Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).

20
doc/src/pair_python.rst
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@ -126,11 +126,11 @@ and *compute_energy*, which both take 3 numerical arguments:
* itype = the (numerical) type of the first atom
* jtype = the (numerical) type of the second atom
This functions need to compute the force and the energy, respectively,
and use the result as return value. The functions need to use the
*pmap* dictionary to convert the LAMMPS atom type number to the symbolic
value of the internal potential parameter data structure. Following
the *LJCutMelt* example, here are the two functions:
This functions need to compute the (scaled) force and the energy,
respectively, and use the result as return value. The functions need
to use the *pmap* dictionary to convert the LAMMPS atom type number
to the symbolic value of the internal potential parameter data structure.
Following the *LJCutMelt* example, here are the two functions:
.. code-block:: python
@ -154,17 +154,17 @@ the *LJCutMelt* example, here are the two functions:
for consistency with the C++ pair styles in LAMMPS, the
*compute_force* function follows the conventions of the Pair::single()
methods and does not return the full force, but the force scaled by
the distance between the two atoms, so this value only needs to be
multiplied by delta x, delta y, and delta z to conveniently obtain the
three components of the force vector between these two atoms.
methods and does not return the pairwise force directly, but the force
divided by the distance between the two atoms, so this value only needs
to be multiplied by delta x, delta y, and delta z to conveniently obtain
the three components of the force vector between these two atoms.
----------
.. note::
The evaluation of scripted python code will slow down the
computation pair-wise interactions quite significantly. However, this
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below

5
doc/src/pair_style.rst
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@ -154,10 +154,10 @@ accelerated styles exist.
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting
* :doc:`dpd/tstat <pair_dpd>` - pairwise DPD thermostatting
* :doc:`dsmc <pair_dsmc>` - Direct Simulation Monte Carlo (DSMC)
* :doc:`e3b <pair_e3b>` - Explicit-three body (E3B) water model
* :doc:`drip <pair_drip>` - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
@ -183,6 +183,7 @@ accelerated styles exist.
* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
* :doc:`gw <pair_gw>` - Gao-Weber potential
* :doc:`gw/zbl <pair_gw>` - Gao-Weber potential with a repulsive ZBL core
* :doc:`harmonic/cut <pair_harmonic_cut>` - repulsive-only harmonic potential
* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential

2
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@ -202,7 +202,7 @@ elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
are usually defined by simple formulas involving two sets of pairwise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the three-body parameters for

6
doc/src/pair_write.rst
View File

@ -76,8 +76,10 @@ must be set before this command can be invoked.
Due to how the pairwise force is computed, an inner value > 0.0 must
be specified even if the potential has a finite value at r = 0.0.
For EAM potentials, the pair_write command only tabulates the
pairwise portion of the potential, not the embedding portion.
The *pair_write* command can only be used for pairwise additive
interactions for which a `Pair::single()` function can be and has
been implemented. This excludes for example manybody potentials
or TIP4P coulomb styles.
Related commands
""""""""""""""""

2
doc/src/run_style.rst
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@ -89,7 +89,7 @@ in its 3d FFTs. In this scenario, splitting your P total processors
into 2 subsets of processors, P1 in the first partition and P2 in the
second partition, can enable your simulation to run faster. This is
because the long-range forces in PPPM can be calculated at the same
time as pair-wise and bonded forces are being calculated, and the FFTs
time as pairwise and bonded forces are being calculated, and the FFTs
can actually speed up when running on fewer processors.
To use this style, you must define 2 partitions where P1 is a multiple

9
doc/src/third_order.rst
View File

@ -1,8 +1,11 @@
.. index:: third_order
.. index:: third_order/kk
third_order command
===================
Accelerator Variants: third_order/kk
Syntax
""""""
@ -49,6 +52,12 @@ If the style eskm is selected, the tensor will be using energy units of 10 J/mol
These units conform to eskm style from the dynamical_matrix command, which
will simplify operations using dynamical matrices with third order tensors.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

5
doc/utils/sphinx-config/false_positives.txt
View File

@ -194,6 +194,7 @@ Baczewski
Bagchi
Bagi
Bagnold
Baig
Bajaj
Bkappa
Bal
@ -668,6 +669,7 @@ Derlet
Deserno
Destree
destructor
destructors
detils
Devanathan
devel
@ -1569,6 +1571,7 @@ ke
KE
Keblinski
Keefe
Keffer
keflag
Keir
Kelchner
@ -2647,6 +2650,7 @@ pscreen
pscrozi
pseudodynamics
pseudopotential
pSp
Pstart
Pstop
pstyle
@ -2925,6 +2929,7 @@ Runge
runtime
Rutuparna
rx
rxd
rxnave
rxnsum
ry

4
examples/PACKAGES/electron_stopping/Si.Si.elstop
View File

@ -1,8 +1,8 @@
# Electronic stopping for Si in Si
# Uses metal units
# Electronic stopping for Si in Si UNITS: metal DATE: 2019-02-19 CONTRIBUTOR: Risto Toijala risto.toijala@helsinki.fi
# Kinetic energy in eV, stopping power in eV/A
# For other atom types, add columns.
# atom type 1
# energy Si in Si
3918.2 6.541
15672.9 13.091

2
examples/PACKAGES/gle/qt-300k.A
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
3.904138445158e-4 4.681059722010e-2 3.079778738058e-2 4.428079381336e-2 5.057825203477e-2 2.591193419597e-2 1.513907125942e-2
-4.789343294190e-2 2.037551040972e-2 6.597801861779e-2 -8.528273506602e-3 -2.230839572773e-3 6.593086307870e-3 -6.653653981891e-2
-2.905096373618e-2 -6.597801861779e-2 2.086885297843e-2 1.145471984072e-2 3.111465343867e-2 1.101562087523e-2 -3.264959166486e-2

2
examples/PACKAGES/gle/qt-300k.C
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
2.999985914100e+2 5.937593337000e+0 2.144376751500e+2 5.883055908000e+1 -1.119803766000e+2 -6.793381764000e+1 1.379789732400e+1
5.937593337000e+0 3.781851303000e+2 -5.794518522000e+1 -2.178772681500e+2 -1.649310659100e+2 -6.557113452000e+1 3.833830743000e+1
2.144376751500e+2 -5.794518522000e+1 7.325759985000e+2 2.188507713000e+2 -3.704586531000e+2 -3.385193865000e+1 -4.827706758000e+0

2
examples/PACKAGES/gle/smart.A
View File

@ -1,3 +1,5 @@
# DATE: 2014-11-24 UNITS: real CONTRIBUTOR: Michele Ceriotti michele.ceriotti@gmail.com
4.247358737218e-3 3.231404593065e-2 -9.715629522215e-3 8.199488441225e-3 7.288427565896e-3 -3.634229949055e-3 -3.294395982200e-3
4.887738278128e-2 5.978602802893e-1 -2.079222967202e-1 1.088740438247e-1 4.666954324786e-2 -1.334147134493e-2 -3.914996645811e-2
4.015863091190e-2 2.079222967202e-1 1.645970119444e-1 8.351952991453e-2 5.114740085468e-2 1.217862237677e-2 -4.506711205974e-2

2
examples/README
View File

@ -94,7 +94,7 @@ msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
numdiff: numerical difference computation of forces
numdiff: numerical difference computation of forces and virial
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter

87
examples/numdiff/in.numdiff
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@ -1,33 +1,74 @@
# Numerical difference calculation of error in forces
# Numerical difference calculation
# of error in forces and virial stress
units metal
atom_style atomic
# adjustable parameters
atom_modify map yes
lattice fcc 5.358000
region box block 0 6 0 6 0 6
create_box 1 box
create_atoms 1 box
mass 1 39.903
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
velocity all create 10 2357 mom yes dist gaussian
units metal
atom_style atomic
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
atom_modify map yes
lattice fcc 5.358000
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
create_box 1 box
create_atoms 1 box
mass 1 39.903
neighbor 1 bin
velocity all create ${temp} 2357 mom yes dist gaussian
timestep 0.001
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
fix numdiff all numdiff 200 0.0001
fix nve all nve
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
variable errx atom fx-f_numdiff[1]
variable erry atom fy-f_numdiff[2]
variable errz atom fz-f_numdiff[3]
timestep 0.001
fix nve all nve
write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]
# define numerical force calculation
dump forces all custom 200 force_error.dump v_errx v_erry v_errz
thermo 200
run 2000
fix numforce all numdiff ${nthermo} ${fdelta}
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + &
v_erryy^2 + &
v_errzz^2 + &
v_erryz^2 + &
v_errxz^2 + &
v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + &
c_myvirial[3]^2 + &
c_myvirial[3]^2 + &
c_myvirial[4]^2 + &
c_myvirial[5]^2 + &
c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
run ${nsteps}

175
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@ -0,0 +1,175 @@
LAMMPS (7 Jan 2022)
# Numerical difference calculation
# of error in forces and virial stress
# adjustable parameters
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
units metal
atom_style atomic
atom_modify map yes
lattice fcc 5.358000
Lattice spacing in x,y,z = 5.358 5.358 5.358
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
region box block 0 3 0 ${nlat} 0 ${nlat}
region box block 0 3 0 3 0 ${nlat}
region box block 0 3 0 3 0 3
create_box 1 box
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
create_atoms CPU = 0.000 seconds
mass 1 39.903
velocity all create ${temp} 2357 mom yes dist gaussian
velocity all create 10.0 2357 mom yes dist gaussian
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
timestep 0.001
fix nve all nve
# define numerical force calculation
fix numforce all numdiff ${nthermo} ${fdelta}
fix numforce all numdiff 10 ${fdelta}
fix numforce all numdiff 10 1.0e-4
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
fix numvirial all numdiff/virial 10 ${vdelta}
fix numvirial all numdiff/virial 10 1.0e-6
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
thermo 10
run ${nsteps}
run 500
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.9407173
ghost atom cutoff = 5.9407173
binsize = 2.9703587, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06
10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07
20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06
30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07
40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08
50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08
60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08
70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08
80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08
90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08
100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08
110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08
120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08
130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08
140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09
150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09
160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09
170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08
180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09
190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09
200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08
210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08
220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09
230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08
240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08
250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08
260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09
270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08
280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08
290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08
300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08
310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08
320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08
330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08
340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08
350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08
360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08
370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08
380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08
390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08
400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08
410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08
420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08
430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08
440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08
450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08
460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08
470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08
480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08
490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08
500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08
Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms
Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17
Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70
Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66
Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51
Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89
Other | | 0.0006258 | | | 0.07
Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 558 ave 558 max 558 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 972 ave 972 max 972 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 972
Ave neighs/atom = 9
Neighbor list builds = 500
Dangerous builds not checked
Total wall time: 0:00:00

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@ -0,0 +1,175 @@
LAMMPS (7 Jan 2022)
# Numerical difference calculation
# of error in forces and virial stress
# adjustable parameters
variable nsteps index 500 # length of run
variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable temp index 10.0 # temperature
units metal
atom_style atomic
atom_modify map yes
lattice fcc 5.358000
Lattice spacing in x,y,z = 5.358 5.358 5.358
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
region box block 0 3 0 ${nlat} 0 ${nlat}
region box block 0 3 0 3 0 ${nlat}
region box block 0 3 0 3 0 3
create_box 1 box
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
create_atoms CPU = 0.000 seconds
mass 1 39.903
velocity all create ${temp} 2357 mom yes dist gaussian
velocity all create 10.0 2357 mom yes dist gaussian
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
timestep 0.001
fix nve all nve
# define numerical force calculation
fix numforce all numdiff ${nthermo} ${fdelta}
fix numforce all numdiff 10 ${fdelta}
fix numforce all numdiff 10 1.0e-4
variable ferrx atom f_numforce[1]-fx
variable ferry atom f_numforce[2]-fy
variable ferrz atom f_numforce[3]-fz
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
compute myvirial all pressure NULL virial
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
fix numvirial all numdiff/virial 10 ${vdelta}
fix numvirial all numdiff/virial 10 1.0e-6
variable errxx equal f_numvirial[1]-c_myvirial[1]
variable erryy equal f_numvirial[2]-c_myvirial[2]
variable errzz equal f_numvirial[3]-c_myvirial[3]
variable erryz equal f_numvirial[4]-c_myvirial[6]
variable errxz equal f_numvirial[5]-c_myvirial[5]
variable errxy equal f_numvirial[6]-c_myvirial[4]
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
thermo ${nthermo}
thermo 10
run ${nsteps}
run 500
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.9407173
ghost atom cutoff = 5.9407173
binsize = 2.9703587, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cubic, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
0 10 -7.0259569 -6.8876486 28.564278 10664.391 9.1481187e-08
10 9.9388179 -7.0251107 -6.8876486 30.21736 1.4771865e-08 1.3452512e-07
20 9.7572185 -7.022599 -6.8876485 35.123527 1.437525e-08 8.0966999e-07
30 9.4606673 -7.0184974 -6.8876484 43.132052 1.4375468e-08 1.990012e-08
40 9.0579092 -7.0129268 -6.8876483 54.000927 1.4350331e-08 1.7239028e-08
50 8.5607685 -7.0060508 -6.8876482 67.403151 1.4353284e-08 7.813181e-09
60 7.9838726 -6.9980717 -6.8876481 82.935358 1.4398078e-08 2.022316e-08
70 7.3442875 -6.9892255 -6.8876479 100.12892 1.434409e-08 7.5938179e-09
80 6.6610579 -6.9797757 -6.8876477 118.46358 1.4324787e-08 7.1972571e-09
90 5.9546462 -6.9700053 -6.8876476 137.38365 1.4322718e-08 4.3978378e-09
100 5.2462727 -6.9602077 -6.8876474 156.31651 1.4273172e-08 4.6728038e-09
110 4.5571706 -6.9506767 -6.8876472 174.69294 1.4266163e-08 3.522225e-09
120 3.9077807 -6.9416949 -6.887647 191.96859 1.42241e-08 3.5357511e-09
130 3.3169241 -6.9335227 -6.8876469 207.64566 1.4203813e-08 2.5182488e-09
140 2.8010028 -6.926387 -6.8876468 221.29333 1.4164215e-08 2.3112509e-09
150 2.3732854 -6.9204712 -6.8876467 232.5658 1.4134122e-08 1.9368963e-09
160 2.0433329 -6.9159076 -6.8876466 241.21647 1.4095473e-08 3.6806452e-09
170 1.8166184 -6.912772 -6.8876466 247.10715 1.4049531e-08 2.5319322e-09
180 1.6943727 -6.9110813 -6.8876467 250.21143 1.3997912e-08 1.952404e-09
190 1.6736731 -6.910795 -6.8876467 250.61203 1.3915487e-08 1.4271767e-09
200 1.7477659 -6.9118199 -6.8876468 248.49223 1.3850618e-08 2.4515718e-09
210 1.9065921 -6.9140167 -6.8876469 244.12226 1.3747916e-08 1.7957531e-09
220 2.1374676 -6.91721 -6.887647 237.84173 1.3674779e-08 2.6613511e-09
230 2.4258607 -6.9211989 -6.8876472 230.0395 1.3565712e-08 3.0777067e-09
240 2.7562034 -6.9257679 -6.8876473 221.13265 1.3440442e-08 1.7111501e-09
250 3.1126827 -6.9306984 -6.8876474 211.54566 1.3270914e-08 1.6690112e-09
260 3.4799641 -6.9357784 -6.8876476 201.69126 1.3105092e-08 2.1637558e-09
270 3.8438148 -6.9408108 -6.8876477 191.95361 1.2962846e-08 4.4613506e-09
280 4.191607 -6.9456212 -6.8876478 182.6745 1.2846383e-08 3.3730203e-09
290 4.5126922 -6.9500621 -6.8876478 174.14285 1.2710692e-08 2.2809889e-09
300 4.7986487 -6.9540172 -6.8876479 166.58747 1.2657778e-08 6.9880891e-09
310 5.0434083 -6.9574025 -6.8876479 160.17316 1.266381e-08 4.2486217e-09
320 5.243275 -6.9601668 -6.8876479 154.99974 1.279856e-08 5.1505673e-09
330 5.3968455 -6.9622908 -6.8876479 151.1038 1.2981831e-08 3.3339333e-09
340 5.5048468 -6.9637845 -6.8876479 148.46296 1.3159021e-08 1.7881393e-09
350 5.569902 -6.9646843 -6.8876479 147.00205 1.3439465e-08 5.6876219e-09
360 5.5962378 -6.9650485 -6.8876478 146.60113 1.3645943e-08 7.233847e-09
370 5.5893468 -6.9649531 -6.8876478 147.10471 1.3829581e-08 4.5514318e-09
380 5.5556199 -6.9644866 -6.8876477 148.33195 1.4005893e-08 4.2971846e-09
390 5.5019639 -6.9637444 -6.8876476 150.08725 1.4157454e-08 3.3564262e-09
400 5.4354239 -6.962824 -6.8876476 152.17073 1.4226422e-08 4.2393923e-09
410 5.3628267 -6.9618199 -6.8876475 154.38825 1.4302679e-08 3.8937698e-09
420 5.2904639 -6.960819 -6.8876475 156.56034 1.4381099e-08 4.315875e-09
430 5.2238282 -6.9598973 -6.8876474 158.52969 1.4426567e-08 4.2658185e-09
440 5.1674149 -6.9591171 -6.8876474 160.16704 1.4453381e-08 5.7055268e-09
450 5.1245913 -6.9585248 -6.8876474 161.37513 1.4449488e-08 4.4308801e-09
460 5.0975361 -6.9581506 -6.8876474 162.09077 1.4445596e-08 5.8269923e-09
470 5.0872416 -6.9580082 -6.8876474 162.28517 1.4444348e-08 4.8263194e-09
480 5.0935712 -6.9580957 -6.8876474 161.96268 1.4411666e-08 6.222228e-09
490 5.115362 -6.9583971 -6.8876474 161.15816 1.4369716e-08 3.3926077e-09
500 5.1505605 -6.958884 -6.8876474 159.9333 1.4288515e-08 3.8845251e-09
Loop time of 0.252598 on 4 procs for 500 steps with 108 atoms
Performance: 171.023 ns/day, 0.140 hours/ns, 1979.430 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021545 | 0.0022845 | 0.0023794 | 0.2 | 0.90
Neigh | 0.0063887 | 0.0067604 | 0.0069752 | 0.3 | 2.68
Comm | 0.01048 | 0.010916 | 0.011408 | 0.3 | 4.32
Output | 0.0026603 | 0.0027399 | 0.0029738 | 0.3 | 1.08
Modify | 0.2295 | 0.22952 | 0.22954 | 0.0 | 90.86
Other | | 0.0003814 | | | 0.15
Nlocal: 27 ave 29 max 25 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 325 ave 327 max 323 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 243 ave 273 max 228 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 972
Ave neighs/atom = 9
Neighbor list builds = 500
Dangerous builds not checked
Total wall time: 0:00:00

18
examples/plugins/angle_zero2.h
View File

@ -21,17 +21,17 @@ namespace LAMMPS_NS {
class AngleZero2 : public Angle {
public:
AngleZero2(class LAMMPS *);
virtual ~AngleZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~AngleZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
double equilibrium_angle(int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int);
double single(int, int, int, int) override;
protected:
double *theta0;

20
examples/plugins/bond_zero2.h
View File

@ -21,18 +21,18 @@ namespace LAMMPS_NS {
class BondZero2 : public Bond {
public:
BondZero2(class LAMMPS *);
virtual ~BondZero2();
virtual void compute(int, int);
virtual void settings(int, char **);
~BondZero2() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void coeff(int, char **) override;
double equilibrium_distance(int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, double, int, int, double &);
virtual void *extract(const char *, int &);
double single(int, double, int, int, double &) override;
void *extract(const char *, int &) override;
protected:
double *r0;

14
examples/plugins/dihedral_zero2.h
View File

@ -25,14 +25,14 @@ namespace LAMMPS_NS {
class DihedralZero2 : public Dihedral {
public:
DihedralZero2(class LAMMPS *);
virtual ~DihedralZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~DihedralZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
protected:
int coeffflag;

23
examples/plugins/fix_nve2.h
View File

@ -11,12 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(nve2, FixNVE2)
#else
#ifndef LMP_FIX_NVE2_H
#define LMP_FIX_NVE2_H
@ -27,14 +21,14 @@ namespace LAMMPS_NS {
class FixNVE2 : public Fix {
public:
FixNVE2(class LAMMPS *, int, char **);
virtual ~FixNVE2() {}
int setmask();
virtual void init();
virtual void initial_integrate(int);
virtual void final_integrate();
virtual void initial_integrate_respa(int, int, int);
virtual void final_integrate_respa(int, int);
virtual void reset_dt();
int setmask() override;
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
void initial_integrate_respa(int, int, int) override;
void final_integrate_respa(int, int) override;
void reset_dt() override;
protected:
double dtv, dtf;
@ -44,7 +38,6 @@ class FixNVE2 : public Fix {
} // namespace LAMMPS_NS
#endif
#endif
/* ERROR/WARNING messages:

14
examples/plugins/improper_zero2.h
View File

@ -21,14 +21,14 @@ namespace LAMMPS_NS {
class ImproperZero2 : public Improper {
public:
ImproperZero2(class LAMMPS *);
virtual ~ImproperZero2();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void settings(int, char **);
~ImproperZero2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void settings(int, char **) override;
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
protected:
int coeffflag;

26
examples/plugins/pair_morse2.h
View File

@ -21,20 +21,20 @@ namespace LAMMPS_NS {
class PairMorse2 : public Pair {
public:
PairMorse2(class LAMMPS *);
virtual ~PairMorse2();
virtual void compute(int, int);
~PairMorse2() override;
void compute(int, int) override;
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
void settings(int, char **) override;
void coeff(int, char **) override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
void *extract(const char *, int &) override;
protected:
double cut_global;

4
examples/plugins/pair_morse2_omp.h
View File

@ -28,8 +28,8 @@ class PairMorse2OMP : public PairMorse2, public ThrOMP {
public:
PairMorse2OMP(class LAMMPS *);
virtual void compute(int, int);
virtual double memory_usage();
void compute(int, int) override;
double memory_usage() override;
private:
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>

26
examples/plugins/pair_zero2.h
View File

@ -31,19 +31,19 @@ namespace LAMMPS_NS {
class PairZero2 : public Pair {
public:
PairZero2(class LAMMPS *);
virtual ~PairZero2();
virtual void compute(int, int);
virtual void compute_outer(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
~PairZero2() override;
void compute(int, int) override;
void compute_outer(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
double single(int, int, int, int, double, double, double, double &) override;
protected:
double cut_global;

2
lib/gpu/Makefile.cuda_mps
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA with the Multi-Process Service (MPS)
# - change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.hip
View File

@ -39,11 +39,9 @@ HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform)
HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler)
ifeq (hcc,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (amd,$(HIP_PLATFORM))
HIP_OPTS += -ffast-math
# possible values: gfx803,gfx900,gfx906
HIP_ARCH = gfx906
else ifeq (nvcc,$(HIP_PLATFORM))

10
lib/gpu/Makefile.linux
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -13,7 +13,7 @@ endif
NVCC = nvcc
# obsolete hardware. not supported by current drivers anymore.
# obsolete hardware. not supported by current drivers and toolkits anymore.
#CUDA_ARCH = -arch=sm_13
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
@ -28,11 +28,11 @@ NVCC = nvcc
#CUDA_ARCH = -arch=sm_37
# Maxwell hardware
CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_52
# Pascal hardware
#CUDA_ARCH = -arch=sm_60
CUDA_ARCH = -arch=sm_60
#CUDA_ARCH = -arch=sm_61
# Volta hardware
@ -70,7 +70,7 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
# GPU binning not recommended with modern GPUs
# GPU binning not recommended for most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

4
lib/gpu/Makefile.linux_multi
View File

@ -1,6 +1,6 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# Generic Linux Makefile for CUDA complied for multiple compute capabilities
# - Add your GPU to CUDA_CODE
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps

1
lib/gpu/Makefile.mpi Symbolic link
View File

@ -0,0 +1 @@
Makefile.linux

10
lib/gpu/Makefile.serial
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# Generic Linux Makefile for CUDA without MPI libraries
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -28,11 +28,11 @@ NVCC = nvcc
#CUDA_ARCH = -arch=sm_37
# Maxwell hardware
CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_50
#CUDA_ARCH = -arch=sm_52
# Pascal hardware
#CUDA_ARCH = -arch=sm_60
CUDA_ARCH = -arch=sm_60
#CUDA_ARCH = -arch=sm_61
# Volta hardware
@ -41,6 +41,10 @@ CUDA_ARCH = -arch=sm_50
# Turing hardware
#CUDA_ARCH = -arch=sm_75
# Ampere hardware
#CUDA_ARCH = -arch=sm_80
#CUDA_ARCH = -arch=sm_86
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL

23
lib/gpu/Makefile.turing
View File

@ -1,23 +0,0 @@
NVCC = $(CUDA_HOME)/bin/nvcc
EXTRAMAKE = Makefile.lammps.standard
CUDA_ARCH = -arch=sm_75
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart
CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include
CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON -DLAMMPS_SMALLBIG
BIN_DIR = .
OBJ_DIR = obj
LIB_DIR = .
AR = ar
BSH = /bin/sh
# GPU binning not recommended with most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

3
lib/kokkos/Makefile.kokkos
View File

@ -1224,6 +1224,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp)
ifeq ($(KOKKOS_INTERNAL_ENABLE_DESUL_ATOMICS), 1)
KOKKOS_SRC += $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_HIP.cpp
endif
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.hpp)
KOKKOS_CXXFLAGS+=$(KOKKOS_INTERNAL_HIP_ARCH_FLAG)

2
lib/kokkos/Makefile.targets
View File

@ -68,6 +68,8 @@ Kokkos_HIP_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
Kokkos_HIP_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
Lock_Array_HIP.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_HIP.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/desul/src/Lock_Array_HIP.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)

2
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Instance.cpp
View File

@ -694,7 +694,7 @@ std::pair<void *, int> CudaInternal::resize_team_scratch_space(
int current_team_scratch = 0;
int zero = 0;
int one = 1;
while (m_team_scratch_pool[current_team_scratch].compare_exchange_weak(
while (!m_team_scratch_pool[current_team_scratch].compare_exchange_weak(
zero, one, std::memory_order_release, std::memory_order_relaxed)) {
current_team_scratch = (current_team_scratch + 1) % m_n_team_scratch;
}

3
python/lammps/core.py
View File

@ -122,6 +122,9 @@ class lammps(object):
for f in os.listdir(winpath)]):
lib_ext = ".dll"
modpath = winpath
elif any([f.startswith('liblammps') and f.endswith('.so')
for f in os.listdir(modpath)]):
lib_ext = ".so"
else:
import platform
if platform.system() == "Darwin":

4
src/.gitignore vendored
View File

@ -429,6 +429,8 @@
/commgrid.h
/compute_ackland_atom.cpp
/compute_ackland_atom.h
/compute_ave_sphere_atom.cpp
/compute_ave_sphere_atom.h
/compute_basal_atom.cpp
/compute_basal_atom.h
/compute_body_local.cpp
@ -1487,6 +1489,8 @@
/pair_dpd_fdt.h
/pair_dpd_fdt_energy.cpp
/pair_dpd_fdt_energy.h
/pair_harmonic_cut.cpp
/pair_harmonic_cut.h
/pair_lennard_mdf.cpp
/pair_lennard_mdf.h
/pair_lj_cut_coul_long_cs.cpp

8
src/ADIOS/dump_atom_adios.h
View File

@ -30,12 +30,12 @@ class DumpAtomADIOS : public DumpAtom {
public:
DumpAtomADIOS(class LAMMPS *, int, char **);
virtual ~DumpAtomADIOS();
~DumpAtomADIOS() override;
protected:
virtual void openfile();
virtual void write();
virtual void init_style();
void openfile() override;
void write() override;
void init_style() override;
private:
DumpAtomADIOSInternal *internal;

8
src/ADIOS/dump_custom_adios.h
View File

@ -29,12 +29,12 @@ class DumpCustomADIOSInternal;
class DumpCustomADIOS : public DumpCustom {
public:
DumpCustomADIOS(class LAMMPS *, int, char **);
virtual ~DumpCustomADIOS();
~DumpCustomADIOS() override;
protected:
virtual void openfile();
virtual void write();
virtual void init_style();
void openfile() override;
void write() override;
void init_style() override;
private:
DumpCustomADIOSInternal *internal;

18
src/ADIOS/reader_adios.h
View File

@ -34,18 +34,18 @@ class ReadADIOSInternal;
class ReaderADIOS : public Reader {
public:
ReaderADIOS(class LAMMPS *);
virtual ~ReaderADIOS();
~ReaderADIOS() override;
virtual void settings(int, char **);
void settings(int, char **) override;
virtual int read_time(bigint &);
virtual void skip();
virtual bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
int &, int &, int &);
virtual void read_atoms(int, int, double **);
int read_time(bigint &) override;
void skip() override;
bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
int &, int &, int &) override;
void read_atoms(int, int, double **) override;
virtual void open_file(const char *);
virtual void close_file();
void open_file(const char *) override;
void close_file() override;
private:
int *fieldindex; // mapping of input fields to dump

4
src/ASPHERE/compute_erotate_asphere.h
View File

@ -27,8 +27,8 @@ namespace LAMMPS_NS {
class ComputeERotateAsphere : public Compute {
public:
ComputeERotateAsphere(class LAMMPS *, int, char **);
void init();
double compute_scalar();
void init() override;
double compute_scalar() override;
private:
double pfactor;

18
src/ASPHERE/compute_temp_asphere.h
View File

@ -27,16 +27,16 @@ namespace LAMMPS_NS {
class ComputeTempAsphere : public Compute {
public:
ComputeTempAsphere(class LAMMPS *, int, char **);
~ComputeTempAsphere();
void init();
void setup();
double compute_scalar();
void compute_vector();
~ComputeTempAsphere() override;
void init() override;
void setup() override;
double compute_scalar() override;
void compute_vector() override;
void remove_bias(int, double *);
void restore_bias(int, double *);
void remove_bias_thr(int, double *, double *);
void restore_bias_thr(int, double *, double *);
void remove_bias(int, double *) override;
void restore_bias(int, double *) override;
void remove_bias_thr(int, double *, double *) override;
void restore_bias_thr(int, double *, double *) override;
private:
int mode;

9
src/ASPHERE/fix_nh_asphere.h
View File

@ -21,16 +21,15 @@ namespace LAMMPS_NS {
class FixNHAsphere : public FixNH {
public:
FixNHAsphere(class LAMMPS *, int, char **);
virtual ~FixNHAsphere() {}
void init();
void init() override;
protected:
double dtq;
class AtomVecEllipsoid *avec;
void nve_v();
void nve_x();
void nh_v_temp();
void nve_v() override;
void nve_x() override;
void nh_v_temp() override;
};
} // namespace LAMMPS_NS

1
src/ASPHERE/fix_nph_asphere.h
View File

@ -27,7 +27,6 @@ namespace LAMMPS_NS {
class FixNPHAsphere : public FixNHAsphere {
public:
FixNPHAsphere(class LAMMPS *, int, char **);
~FixNPHAsphere() {}
};
} // namespace LAMMPS_NS

1
src/ASPHERE/fix_npt_asphere.h
View File

@ -27,7 +27,6 @@ namespace LAMMPS_NS {
class FixNPTAsphere : public FixNHAsphere {
public:
FixNPTAsphere(class LAMMPS *, int, char **);
~FixNPTAsphere() {}
};
} // namespace LAMMPS_NS

6
src/ASPHERE/fix_nve_asphere.h
View File

@ -27,9 +27,9 @@ namespace LAMMPS_NS {
class FixNVEAsphere : public FixNVE {
public:
FixNVEAsphere(class LAMMPS *, int, char **);
void init();
void initial_integrate(int);
void final_integrate();
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
private:
double dtq;

4
src/ASPHERE/fix_nve_asphere_noforce.h
View File

@ -27,8 +27,8 @@ namespace LAMMPS_NS {
class FixNVEAsphereNoforce : public FixNVENoforce {
public:
FixNVEAsphereNoforce(class LAMMPS *, int, char **);
void initial_integrate(int);
void init();
void initial_integrate(int) override;
void init() override;
private:
double dtq;

9
src/ASPHERE/fix_nve_line.h
View File

@ -27,11 +27,10 @@ namespace LAMMPS_NS {
class FixNVELine : public FixNVE {
public:
FixNVELine(class LAMMPS *, int, char **);
~FixNVELine() {}
int setmask();
void init();
void initial_integrate(int);
void final_integrate();
int setmask() override;
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
private:
double MINUSPI, TWOPI;

9
src/ASPHERE/fix_nve_tri.h
View File

@ -27,11 +27,10 @@ namespace LAMMPS_NS {
class FixNVETri : public FixNVE {
public:
FixNVETri(class LAMMPS *, int, char **);
~FixNVETri() {}
int setmask();
void init();
void initial_integrate(int);
void final_integrate();
int setmask() override;
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
private:
double dtq;

1
src/ASPHERE/fix_nvt_asphere.h
View File

@ -27,7 +27,6 @@ namespace LAMMPS_NS {
class FixNVTAsphere : public FixNHAsphere {
public:
FixNVTAsphere(class LAMMPS *, int, char **);
~FixNVTAsphere() {}
};
} // namespace LAMMPS_NS

14
src/ASPHERE/pair_gayberne.cpp
View File

@ -18,18 +18,18 @@
#include "pair_gayberne.h"
#include <cmath>
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "citeme.h"
#include "memory.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;

24
src/ASPHERE/pair_gayberne.h
View File

@ -27,18 +27,18 @@ namespace LAMMPS_NS {
class PairGayBerne : public Pair {
public:
PairGayBerne(LAMMPS *lmp);
virtual ~PairGayBerne();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
~PairGayBerne() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void write_data(FILE *) override;
void write_data_all(FILE *) override;
protected:
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };

12
src/ASPHERE/pair_line_lj.h
View File

@ -27,12 +27,12 @@ namespace LAMMPS_NS {
class PairLineLJ : public Pair {
public:
PairLineLJ(class LAMMPS *);
virtual ~PairLineLJ();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
~PairLineLJ() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
protected:
double cut_global;

20
src/ASPHERE/pair_resquared.h
View File

@ -27,16 +27,16 @@ namespace LAMMPS_NS {
class PairRESquared : public Pair {
public:
PairRESquared(LAMMPS *lmp);
virtual ~PairRESquared();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
~PairRESquared() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
protected:
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };

12
src/ASPHERE/pair_tri_lj.h
View File

@ -27,12 +27,12 @@ namespace LAMMPS_NS {
class PairTriLJ : public Pair {
public:
PairTriLJ(class LAMMPS *);
virtual ~PairTriLJ();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
double init_one(int, int);
~PairTriLJ() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
double init_one(int, int) override;
protected:
double cut_global;

74
src/ATC/fix_atc.h
View File

@ -37,91 +37,91 @@ class FixATC : public Fix {
public:
/** constructor & destructor */
FixATC(class LAMMPS *, int, char **);
~FixATC();
~FixATC() override;
/** initialization functions */
void init();
void init_list(int id, NeighList *ptr);
void setup(int vflag);
void min_setup(int vflag);
void init() override;
void init_list(int id, NeighList *ptr) override;
void setup(int vflag) override;
void min_setup(int vflag) override;
/** setmask: tell LAMMPS which fix methods to call */
int setmask();
int setmask() override;
/** initial_integrate */
void initial_integrate(int vflag);
void initial_integrate(int vflag) override;
/** after first integrate phase */
void post_integrate();
void post_integrate() override;
/** final_integrate */
void final_integrate();
void final_integrate() override;
/** end of step for run or minimize */
void end_of_step();
void end_of_step() override;
/** pre_exchange is used to modify fix-specific data
and is called before domain->pbc() and comm->exchange(). */
void setup_pre_exchange();
void pre_exchange();
void min_pre_exchange();
void setup_pre_exchange() override;
void pre_exchange() override;
void min_pre_exchange() override;
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
double memory_usage() override;
void grow_arrays(int) override;
void copy_arrays(int, int, int) override;
/** pack_exchange called from atom_vec->pack_exchange()
and packs fix-specific data for a given real (local)
atom being sent to another processor. */
int pack_exchange(int, double *);
int pack_exchange(int, double *) override;
/** unpack_exchange called from atom_vec->unpack_exchange()
and unpacks fix-specific data for a given real (local)
atom received from another processor. */
int unpack_exchange(int, double *);
int unpack_exchange(int, double *) override;
/** pack_comm called from comm->forward_comm_fix and
packs fix-specific data for a given ghost atom
from exchange with another proc */
int pack_forward_comm(int, int *, double *, int, int *);
int pack_forward_comm(int, int *, double *, int, int *) override;
/** unpack_comm called from comm->forward_comm_fix and
unpacks fix-specific data for a given ghost atom
from exchange with another proc */
void unpack_forward_comm(int, int, double *);
void unpack_forward_comm(int, int, double *) override;
/** pre_neighbor is used to modify fix-specific data
and is called before neighbor list is built in
neighbor->build(). */
void pre_neighbor();
void setup_pre_neighbor();
void pre_neighbor() override;
void setup_pre_neighbor() override;
/** pre/post_force is used to modify fix-specific data
and is before/after the various force computations. */
void pre_force(int vflag);
void post_force(int vflag);
void pre_force(int vflag) override;
void post_force(int vflag) override;
/** post_run is called after a run completes */
void post_run();
void post_run() override;
/** min_pre_force is called before forces are calculated in minimize */
void min_pre_force(int vflag);
void min_pre_force(int vflag) override;
/** min_post_force is called after forces are calculated in minimize */
void min_post_force(int vflag);
void min_post_force(int vflag) override;
/** modify atc parameters (parser) */
int modify_param(int narg, char **arg);
int modify_param(int narg, char **arg) override;
/** calls ATC_Method to handle restarting/checkpointing */
/** these four methods are for writing per-atom quantities */
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
int pack_restart(int, double *) override;
void unpack_restart(int, int) override;
int size_restart(int) override;
int maxsize_restart() override;
/** these two methods are for writing all other quantities */
void write_restart(FILE *);
void restart(char *);
void write_restart(FILE *) override;
void restart(char *) override;
/** accessor function for ATC_Method class pointer */
const ATC::ATC_Method *atc() { return atc_; }
@ -130,9 +130,9 @@ class FixATC : public Fix {
LAMMPS *lammps_;
/** functions for "thermo" output */
virtual double compute_scalar();
virtual double compute_vector(int n);
virtual double compute_array(int irow, int icol);
double compute_scalar() override;
double compute_vector(int n) override;
double compute_array(int irow, int icol) override;
double dtv, dtf;
ATC::ATC_Method *atc_;
};

12
src/AWPMD/atom_vec_wavepacket.h
View File

@ -28,12 +28,12 @@ class AtomVecWavepacket : public AtomVec {
public:
AtomVecWavepacket(class LAMMPS *);
void grow_pointers();
void force_clear(int, size_t);
void create_atom_post(int);
void data_atom_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);
void grow_pointers() override;
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
void pack_property_atom(int, double *, int, int) override;
private:
int *spin;

14
src/AWPMD/fix_nve_awpmd.h
View File

@ -31,13 +31,13 @@ namespace LAMMPS_NS {
class FixNVEAwpmd : public Fix {
public:
FixNVEAwpmd(class LAMMPS *, int, char **);
int setmask();
virtual void init();
virtual void initial_integrate(int);
virtual void final_integrate();
void initial_integrate_respa(int, int, int);
void final_integrate_respa(int, int);
void reset_dt();
int setmask() override;
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
void initial_integrate_respa(int, int, int) override;
void final_integrate_respa(int, int) override;
void reset_dt() override;
protected:
double dtv, dtf;

28
src/AWPMD/pair_awpmd_cut.h
View File

@ -34,22 +34,22 @@ class PairAWPMDCut : public Pair {
public:
PairAWPMDCut(class LAMMPS *);
virtual ~PairAWPMDCut();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
void init_style();
~PairAWPMDCut() override;
void compute(int, int) override;
void settings(int, char **) override;
void coeff(int, char **) override;
void init_style() override;
void min_pointers(double **, double **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
double init_one(int, int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_restart_settings(FILE *) override;
void read_restart_settings(FILE *) override;
void min_xf_pointers(int, double **, double **);
void min_xf_get(int);
void min_x_set(int);
double memory_usage();
void min_xf_pointers(int, double **, double **) override;
void min_xf_get(int) override;
void min_x_set(int) override;
double memory_usage() override;
private:
int flexible_pressure_flag;

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