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Merge branch 'develop' into Elastic_stress

This commit is contained in:
Axel Kohlmeyer 2022-04-23 04:35:23 -04:00
parent a6f2f04664 7bfa368d8d
commit 31470819c0
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GPG Key ID: D9B44E93BF0C375A
138 changed files with 2294 additions and 2361 deletions
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23
cmake/CMakeLists.txt
View File

@ -105,8 +105,28 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
endif()
endif()
# silence excessive warnings for new Intel Compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare")
endif()
# silence excessive warnings for PGI/NVHPC compilers
if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI"))
set(CMAKE_TUNE_DEFAULT "-Minform=severe")
endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
endif()
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
set(CMAKE_CXX_STANDARD 11)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
endif()
@ -468,6 +488,7 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(lammps PRIVATE ${_FLAG})
target_compile_options(lmp PRIVATE ${_FLAG})
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #

4
cmake/Modules/Documentation.cmake
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@ -7,13 +7,13 @@ if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv -p ${PYTHON_EXECUTABLE})
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
endif()
find_package(Doxygen 1.8.10 REQUIRED)

4
cmake/Modules/Packages/COLVARS.cmake
View File

@ -19,6 +19,10 @@ endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(colvars PRIVATE ${_FLAG})
endforeach()
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
# The line below is needed to locate math_eigen_impl.h

2
cmake/Modules/Packages/MACHDYN.cmake
View File

@ -36,3 +36,5 @@ endif()
if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
endif()
target_compile_definitions(lammps PRIVATE -DEIGEN_NO_CUDA)

4
cmake/presets/kokkos-cuda.cmake
View File

@ -5,7 +5,5 @@ set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

2
cmake/presets/pgi.cmake
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@ -1,4 +1,4 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# preset that will enable PGI (Nvidia) compilers with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "pgc++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "pgcc" CACHE STRING "" FORCE)

13
doc/Makefile
View File

@ -14,23 +14,22 @@ ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
PYTHON = $(shell which python3)
DOXYGEN = $(shell which doxygen)
VIRTUALENV = virtualenv
PYTHON = $(word 3,$(shell type python3))
DOXYGEN = $(word 3,$(shell type doxygen))
HAS_PYTHON3 = NO
HAS_DOXYGEN = NO
HAS_PDFLATEX = NO
ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
HAS_PYTHON3 = YES
endif
ifeq ($(shell which doxygen >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type doxygen >/dev/null 2>&1; echo $$?), 0)
HAS_DOXYGEN = YES
endif
ifeq ($(shell which pdflatex >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell which latexmk >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
HAS_PDFLATEX = YES
endif
endif

3
doc/src/Developer_utils.rst
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@ -211,6 +211,9 @@ Convenience functions
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: errorurl
:project: progguide
.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
:project: progguide

1
doc/src/Errors.rst
View File

@ -11,6 +11,7 @@ them.
:maxdepth: 1
Errors_common
Errors_details
Errors_bugs
Errors_debug
Errors_messages

27
doc/src/Errors_details.rst Normal file
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@ -0,0 +1,27 @@
Detailed discussion of errors and warnings
==========================================
Many errors or warnings are self-explanatory and thus straightforward to
resolve. However, there are also cases, where there is no single cause
and explanation, where LAMMPS can only detect symptoms of an error but
not the exact cause, or where the explanation needs to be more detailed than
what can be fit into a message printed by the program. The following are
discussions of such cases.
.. _err0001:
Unknown identifier in data file
-------------------------------
This error happens when LAMMPS encounters a line of text in an unexpected format
while reading a data file. This is most commonly cause by inconsistent header and
section data. The header section informs LAMMPS how many entries or lines are expected in the
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
or stop reading before the section has ended.
Such a mismatch can happen unexpectedly when the first line of the data
is *not* a comment as required by the format. That would result in
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
is treated as a comment.

81
doc/src/Modify_atom.rst
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@ -9,34 +9,34 @@ A new atom style can be created if one of the existing atom styles
does not define all the attributes you need to store and communicate
with atoms.
Atom_vec_atomic.cpp is the simplest example of an atom style.
The file ``atom_vec_atomic.cpp`` is the simplest example of an atom style.
Examining the code for others will make these instructions more clear.
Note that the :doc:`atom style hybrid <atom_style>` command can be
used to define atoms or particles which have the union of properties
of individual styles. Also the :doc:`fix property/atom <fix_property_atom>`
command can be used to add a single property (e.g. charge
or a molecule ID) to a style that does not have it. It can also be
used to add custom properties to an atom, with options to communicate
them with ghost atoms or read them from a data file. Other LAMMPS
commands can access these custom properties, as can new pair, fix,
compute styles that are written to work with these properties. For
Note that the :doc:`atom style hybrid <atom_style>` command can be used
to define atoms or particles which have the union of properties of
individual styles. Also the :doc:`fix property/atom
<fix_property_atom>` command can be used to add a single property
(e.g. charge or a molecule ID) to a style that does not have it. It can
also be used to add custom properties to an atom, with options to
communicate them with ghost atoms or read them from a data file. Other
LAMMPS commands can access these custom properties, as can new pair,
fix, compute styles that are written to work with these properties. For
example, the :doc:`set <set>` command can be used to set the values of
custom per-atom properties from an input script. All of these methods
are less work than writing code for a new atom style.
are less work than writing and testing(!) code for a new atom style.
If you follow these directions your new style will automatically work
in tandem with others via the :doc:`atom_style hybrid <atom_style>`
command.
The first step is to define a set of strings in the constructor of the
new derived class. Each string will have zero or more space-separated
variable names which are identical to those used in the atom.h header
file for per-atom properties. Note that some represent per-atom
The first step is to define a set of string lists in the constructor of
the new derived class. Each list will have zero or more comma-separated
strings that correspond to the variable names used in the ``atom.h``
header file for per-atom properties. Note that some represent per-atom
vectors (q, molecule) while other are per-atom arrays (x,v). For all
but the last 2 strings you do not need to specify any of
but the last two lists you do not need to specify any of
(id,type,x,v,f). Those are included automatically as needed in the
other strings.
other lists.
.. list-table::
@ -65,16 +65,16 @@ other strings.
* - fields_data_vel
- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
In these strings you can list variable names which LAMMPS already
defines (in some other atom style), or you can create new variable
names. You should not re-use a LAMMPS variable for something with
different meaning in your atom style. If the meaning is related, but
interpreted differently by your atom style, then using the same
variable name means a user should not use your style and the other
style together in a :doc:`atom_style hybrid <atom_style>` command.
Because there will only be one value of the variable and different
parts of LAMMPS will then likely use it differently. LAMMPS has
no way of checking for this.
In these lists you can list variable names which LAMMPS already defines
(in some other atom style), or you can create new variable names. You
should not re-use a LAMMPS variable in your atom style that is used for
something with a different meaning in another atom style. If the
meaning is related, but interpreted differently by your atom style, then
using the same variable name means a user must not use your style and
the other style together in a :doc:`atom_style hybrid <atom_style>`
command. Because there will only be one value of the variable and
different parts of LAMMPS will then likely use it differently. LAMMPS
has no way of checking for this.
If you are defining new variable names then make them descriptive and
unique to your new atom style. For example choosing "e" for energy is
@ -85,32 +85,31 @@ If any of the variable names in your new atom style do not exist in
LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
Search for the word "customize" or "customization" in these 2 files to
see where to add your variable. Adding a flag to the 2nd
customization section in atom.h is only necessary if your code (e.g. a
pair style) needs to check that a per-atom property is defined. These
flags should also be set in the constructor of the atom style child
class.
see where to add your variable. Adding a flag to the 2nd customization
section in ``atom.h`` is only necessary if your code (e.g. a pair style)
needs to check that a per-atom property is defined. These flags should
also be set in the constructor of the atom style child class.
In atom.cpp, aside from the constructor and destructor, there are 3
In ``atom.cpp``, aside from the constructor and destructor, there are 3
methods that a new variable name or flag needs to be added to.
In Atom::peratom_create() when using the add_peratom() method, a
final length argument of 0 is for per-atom vectors, a length > 1 is
for per-atom arrays. Note the use of an extra per-thread flag and the
add_peratom_vary() method when last dimension of the array is
In ``Atom::peratom_create()`` when using the ``Atom::add_peratom()``
method, a cols argument of 0 is for per-atom vectors, a length >
1 is for per-atom arrays. Note the use of the extra per-thread flag and
the add_peratom_vary() method when last dimension of the array is
variable-length.
Adding the variable name to Atom::extract() enable the per-atom data
Adding the variable name to Atom::extract() enables the per-atom data
to be accessed through the :doc:`LAMMPS library interface
<Howto_library>` by a calling code, including from :doc:`Python
<Python_head>`.
The constructor of the new atom style will also typically set a few
flags which are defined at the top of atom_vec.h. If these are
flags which are defined at the top of ``atom_vec.h``. If these are
unclear, see how other atom styles use them.
The grow_pointers() method is also required to make
a copy of peratom data pointers, as explained in the code.
The grow_pointers() method is also required to make a copy of peratom
data pointers, as explained in the code.
There are a number of other optional methods which your atom style can
implement. These are only needed if you need to do something

7
doc/src/compute_rigid_local.rst
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@ -127,19 +127,16 @@ The *vx*, *vy*, *vz*, *fx*, *fy*, *fz* attributes are components of
the COM velocity and force on the COM of the body.
The *omegax*, *omegay*, and *omegaz* attributes are the angular
velocity components of the body around its COM.
velocity components of the body in the system frame around its COM.
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
momentum components of the body around its COM.
momentum components of the body in the system frame around its COM.
The *quatw*, *quati*, *quatj*, and *quatk* attributes are the
components of the 4-vector quaternion representing the orientation of
the rigid body. See the :doc:`set <set>` command for an explanation of
the quaternion vector.
The *angmomx*, *angmomy*, and *angmomz* attributes are the angular
momentum components of the body around its COM.
The *tqx*, *tqy*, *tqz* attributes are components of the torque acting
on the body around its COM.

45
doc/src/compute_temp_profile.rst
View File

@ -76,21 +76,28 @@ velocity for each atom. Note that if there is only one atom in the
bin, its thermal velocity will thus be 0.0.
After the spatially-averaged velocity field has been subtracted from
each atom, the temperature is calculated by the formula KE = (dim\*N
- dim\*Nx\*Ny\*Nz) k T/2, where KE = total kinetic energy of the group of
atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
simulation, N = number of atoms in the group, k = Boltzmann constant,
and T = temperature. The dim\*Nx\*Ny\*Nz term are degrees of freedom
subtracted to adjust for the removal of the center-of-mass velocity in
each of Nx\*Ny\*Nz bins, as discussed in the :ref:`(Evans) <Evans1>` paper.
each atom, the temperature is calculated by the formula
*KE* = (*dim\*N* - *Ns\*Nx\*Ny\*Nz* - *extra* ) *k* *T*/2, where *KE* = total
kinetic energy of the group of atoms (sum of 1/2 *m* *v*\^2), *dim* = 2
or 3 = dimensionality of the simulation, *Ns* = 0, 1, 2 or 3 for
streaming velocity subtracted in 0, 1, 2 or 3 dimensions, *extra* = extra
degrees-of-freedom, *N* = number of atoms in the group, *k* = Boltzmann
constant, and *T* = temperature. The *Ns\*Nx\*Ny\*Nz* term is degrees
of freedom subtracted to adjust for the removal of the center-of-mass
velocity in each direction of the *Nx\*Ny\*Nz* bins, as discussed in the
:ref:`(Evans) <Evans1>` paper. The extra term defaults to (*dim* - *Ns*)
and accounts for overall conservation of center-of-mass velocity across
the group in directions where streaming velocity is *not* subtracted. This
can be altered using the *extra* option of the
:doc:`compute_modify <compute_modify>` command.
If the *out* keyword is used with a *tensor* value, which is the
default, a kinetic energy tensor, stored as a 6-element vector, is
also calculated by this compute for use in the computation of a
pressure tensor. The formula for the components of the tensor is the
same as the above formula, except that v\^2 is replaced by vx\*vy for
the xy component, etc. The 6 components of the vector are ordered xx,
yy, zz, xy, xz, yz.
same as the above formula, except that *v*\^2 is replaced by *vx\*vy* for
the xy component, etc. The 6 components of the vector are ordered *xx,
yy, zz, xy, xz, yz.*
If the *out* keyword is used with a *bin* value, the count of atoms
and computed temperature for each bin are stored for output, as an
@ -123,10 +130,20 @@ needed, the subtracted degrees-of-freedom can be altered using the
.. note::
When using the *out* keyword with a value of *bin*, the
calculated temperature for each bin does not include the
degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the *extra* option, which is applied to each bin.
calculated temperature for each bin includes the degrees-of-freedom
adjustment described in the preceding paragraph for fixes that
constrain molecular motion, as well as the adjustment due to
the *extra* option (which defaults to *dim* - *Ns* as described above),
by fractionally applying them based on the fraction of atoms in each
bin. As a result, the bin degrees-of-freedom summed over all bins exactly
equals the degrees-of-freedom used in the scalar temperature calculation,
:math:`\Sigma N_{DOF_i} = N_{DOF}` and the corresponding relation for temperature
is also satisfied :math:`\Sigma N_{DOF_i} T_i = N_{DOF} T`.
These relations will breakdown in cases where the adjustment
exceeds the actual number of degrees-of-freedom in a bin. This could happen
if a bin is empty or in situations where rigid molecules
are non-uniformly distributed, in which case the reported
temperature within a bin may not be accurate.
See the :doc:`Howto thermostat <Howto_thermostat>` page for a
discussion of different ways to compute temperature and perform

87
doc/src/fix_adapt.rst
View File

@ -14,7 +14,7 @@ Syntax
* adapt = style name of this fix command
* N = adapt simulation settings every this many timesteps
* one or more attribute/arg pairs may be appended
* attribute = *pair* or *bond* or *kspace* or *atom*
* attribute = *pair* or *bond* or *angle* or *kspace* or *atom*
.. parsed-literal::
@ -28,11 +28,16 @@ Syntax
bparam = parameter to adapt over time
I = type bond to set parameter for
v_name = variable with name that calculates value of bparam
*angle* args = astyle aparam I v_name
astyle = angle style name, e.g. harmonic
aparam = parameter to adapt over time
I = type angle to set parameter for
v_name = variable with name that calculates value of aparam
*kspace* arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
*atom* args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam
*atom* args = atomparam v_name
atomparam = parameter to adapt over time
v_name = variable with name that calculates value of atomparam
* zero or more keyword/value pairs may be appended
* keyword = *scale* or *reset* or *mass*
@ -283,30 +288,62 @@ operates. The only difference is that now a bond coefficient for a
given bond type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the bond type argument to set the coefficients for multiple bond types.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to N (inclusive). A middle
asterisk means all types from m to n (inclusive).
the bond type argument to set the coefficients for multiple bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The only bonds that currently are
working with fix_adapt are
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
+------------------------------------+-------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`fene <bond_fene>` | k, r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`gromos <bond_gromos>` | k, r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`nonlinear <bond_nonlinear>` | r0 | type bonds |
+------------------------------------+-------+------------+
+------------------------------------+-------+-----------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`fene/nm <bond_fene_nm>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+------------------------------------+-------+-----------------+
----------
The *angle* keyword uses the specified variable to change the value of
an angle coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now an angle coefficient for a
given angle type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the angle type argument to set the coefficients for multiple angle
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of angle types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+-------+-----------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+-------+-----------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.
----------

6
doc/src/fix_nve.rst
View File

@ -35,6 +35,10 @@ consistent with the microcanonical ensemble (NVE) provided there
are (full) periodic boundary conditions and no other "manipulations"
of the system (e.g. fixes that modify forces or velocities).
This fix invokes the velocity form of the
Störmer-Verlet time integration algorithm (velocity-Verlet). Other
time integration options can be invoked using the :doc:`run_style <run_style>` command.
----------
.. include:: accel_styles.rst
@ -57,7 +61,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`run_style <run_style>`
Default
"""""""

16
doc/src/fix_property_atom.rst
View File

@ -304,13 +304,15 @@ uninterrupted fashion.
.. warning::
When reading data from a restart file, this fix command has to be
specified **exactly** the same was in the input script that created
the restart file. LAMMPS will only check whether a fix is of the
same style and has the same fix ID and in case of a match will then
try to initialize the fix with the data stored in the binary
restart file. If the names and associated date types in the new
fix property/atom command do not match the old one exactly, data
can be corrupted or LAMMPS may crash.
specified **after** the *read_restart* command and **exactly** the
same was in the input script that created the restart file. LAMMPS
will only check whether a fix is of the same style and has the same
fix ID and in case of a match will then try to initialize the fix
with the data stored in the binary restart file. If the names and
associated date types in the new fix property/atom command do not
match the old one exactly, data can be corrupted or LAMMPS may crash.
If the fix is specified **before** the *read_restart* command its
data will not be restored.
None of the :doc:`fix_modify <fix_modify>` options are relevant to
this fix. No global or per-atom quantities are stored by this fix for

2
doc/src/fix_ttm.rst
View File

@ -217,7 +217,7 @@ units used.
.. note::
The electronic temperature at each grid point must be a non-zero
positive value, both initially, and as the temperature evovles over
positive value, both initially, and as the temperature evolves over
time. Thus you must use either the *set* or *infile* keyword or be
restarting a simulation that used this fix previously.

16
doc/src/group.rst
View File

@ -258,11 +258,17 @@ assignment is made at the beginning of the minimization, but not
during the iterations of the minimizer.
The point in the timestep at which atoms are assigned to a dynamic
group is after the initial stage of velocity Verlet time integration
has been performed, and before neighbor lists or forces are computed.
This is the point in the timestep where atom positions have just
changed due to the time integration, so the region criterion should be
accurate, if applied.
group is after interatomic forces have been computed, but before any
fixes which alter forces or otherwise update the system have been
invoked. This means that atom positions have been updated, neighbor
lists and ghost atoms are current, and both intermolecular and
intramolecular forces have been calculated based on the new
coordinates. Thus the region criterion, if applied, should be
accurate. Also, any computes invoked by an atom-style variable should
use updated information for that timestep, e.g. potential energy/atom
or coordination number/atom. Similarly, fixes or computes which are
invoked after that point in the timestep, should operate on the new
group of atoms.
.. note::

3
doc/src/run_style.rst
View File

@ -67,7 +67,8 @@ Description
Choose the style of time integrator used for molecular dynamics
simulations performed by LAMMPS.
The *verlet* style is a standard velocity-Verlet integrator.
The *verlet* style is the velocity form of the
Störmer-Verlet time integration algorithm (velocity-Verlet)
----------

2
doc/src/thermo_modify.rst
View File

@ -252,6 +252,6 @@ flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",
"%10d", and "%12.8g". For style "multi", the line and format defaults
"%10d", and "%14.8g". For style "multi", the line and format defaults
are "multi", "%14d", and "%14.4f". For style "yaml", the line and format
defaults are "%d" and "%.15g".

2
doc/src/thermo_style.rst
View File

@ -10,7 +10,7 @@ Syntax
thermo_style style args
* style = *one* or *multi* *yaml* or *custom*
* style = *one* or *multi* or *yaml* or *custom*
* args = list of arguments for a particular style
.. parsed-literal::

1
doc/utils/requirements.txt
View File

@ -6,3 +6,4 @@ breathe
Pygments
six
pyyaml
wheel

78
src/AWPMD/atom_vec_wavepacket.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -20,8 +19,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -32,33 +29,29 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
molecular = Atom::ATOMIC;
forceclearflag = 1;
atom->wavepacket_flag = 1;
atom->electron_flag = 1; // compatible with eff
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag =
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
atom->wavepacket_flag = atom->q_flag = atom->spin_flag = atom->eradius_flag = 1;
atom->ervel_flag = atom->erforce_flag = atom->cs_flag = atom->csforce_flag = 1;
atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q spin eradius ervel erforce cs csforce "
"vforce ervelforce etag";
fields_copy = (char *) "q spin eradius ervel cs etag";
fields_comm = (char *) "eradius";
fields_comm_vel = (char *) "eradius ervel cs";
fields_reverse = (char *) "erforce ervelforce vforce csforce";
fields_border = (char *) "q spin eradius etag";
fields_border_vel = (char *) "q spin eradius etag ervel cs";
fields_exchange = (char *) "q spin eradius ervel etag cs";
fields_restart = (char *) "q spin eradius ervel etag cs";
fields_create = (char *) "q spin eradius ervel etag cs";
fields_data_atom = (char *) "id type q spin eradius etag cs x";
fields_data_vel = (char *) "id v ervel";
fields_grow = {"q", "spin", "eradius", "ervel", "erforce",
"cs", "csforce", "vforce", "ervelforce", "etag"};
fields_copy = {"q", "spin", "eradius", "ervel", "cs", "etag"};
fields_comm = {"eradius"};
fields_comm_vel = {"eradius", "ervel", "cs"};
fields_reverse = {"erforce", "ervelforce", "vforce", "csforce"};
fields_border = {"q", "spin", "eradius", "etag"};
fields_border_vel = {"q", "spin", "eradius", "etag", "ervel", "cs"};
fields_exchange = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_restart = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_create = {"q", "spin", "eradius", "ervel", "etag", "cs"};
fields_data_atom = {"id", "type", "q", "spin", "eradius", "etag", "cs", "x"};
fields_data_vel = {"id", "v", "ervel"};
setup_fields();
}
@ -84,7 +77,7 @@ void AtomVecWavepacket::grow_pointers()
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
memset(&erforce[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -112,12 +105,12 @@ void AtomVecWavepacket::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecWavepacket::property_atom(char *name)
int AtomVecWavepacket::property_atom(const std::string &name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
if (name == "spin") return 0;
if (name == "eradius") return 1;
if (name == "ervel") return 2;
if (name == "erforce") return 3;
return -1;
}
@ -126,34 +119,41 @@ int AtomVecWavepacket::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecWavepacket::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = spin[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = eradius[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ervel[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = erforce[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/AWPMD/atom_vec_wavepacket.h
View File

@ -32,7 +32,7 @@ class AtomVecWavepacket : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

49
src/BPM/atom_vec_bpm_sphere.cpp
View File

@ -14,6 +14,7 @@
#include "atom_vec_bpm_sphere.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "fix.h"
#include "fix_adapt.h"
@ -43,23 +44,21 @@ AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
// clang-format off
fields_grow = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega torque quat";
fields_copy = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega quat";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega quat";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega quat";
fields_exchange = (char *) "molecule num_bond bond_type bond_atom nspecial special radius rmass "
"omega quat";
fields_restart = (char *) "molecule num_bond bond_type bond_atom radius rmass omega quat";
fields_create = (char *) "molecule num_bond nspecial radius rmass omega quat";
fields_data_atom = (char *) "id molecule type radius rmass x";
fields_data_vel = (char *) "id v omega";
// clang-format on
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special",
"radius", "rmass", "omega", "torque", "quat"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
"special", "radius", "rmass", "omega", "quat"};
fields_comm_vel = {"omega", "quat"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega", "quat"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial",
"special", "radius", "rmass", "omega", "quat"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom",
"radius", "rmass", "omega", "quat"};
fields_create = {"molecule", "num_bond", "nspecial", "radius", "rmass", "omega", "quat"};
fields_data_atom = {"id", "molecule", "type", "radius", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
bond_per_atom = 0;
bond_negative = NULL;
@ -83,8 +82,8 @@ void AtomVecBPMSphere::process_args(int narg, char **arg)
// dynamic particle radius and mass must be communicated every step
if (radvary) {
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
fields_comm = {"radius", "rmass"};
fields_comm_vel = {"radius", "rmass", "omega"};
}
// delay setting up of fields until now
@ -100,12 +99,16 @@ void AtomVecBPMSphere::init()
// check if optional radvary setting should have been set to 1
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style, "adapt") == 0) {
FixAdapt *fix = (FixAdapt *) modify->fix[i];
if (fix->diamflag && radvary == 0)
for (auto ifix : modify->get_fix_by_style("^adapt")) {
if (radvary == 0) {
if ((strcmp(ifix->style, "adapt") == 0) && (dynamic_cast<FixAdapt *>(ifix)->diamflag))
error->all(FLERR, "Fix adapt changes atom radii but atom_style bpm/sphere is not dynamic");
// cannot properly check for fix adapt/fep since its header is optional
if ((strcmp(ifix->style, "adapt/fep") == 0) && (comm->me == 0))
error->warning(
FLERR, "Fix adapt/fep may change atom radii but atom_style bpm/sphere is not dynamic");
}
}
}
/* ----------------------------------------------------------------------

2
src/BPM/atom_vec_bpm_sphere.h
View File

@ -45,7 +45,7 @@ class AtomVecBPMSphere : public AtomVec {
int **nspecial;
double *radius, *rmass;
double **omega, **torque, **quat;
double **omega, **quat;
int any_bond_negative;
int bond_per_atom;

8
src/BPM/pair_bpm_spring.cpp
View File

@ -253,13 +253,13 @@ void PairBPMSpring::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j], sizeof(int), 1, fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
fread(&k[i][j], sizeof(double), 1, fp);
fread(&cut[i][j], sizeof(double), 1, fp);
fread(&gamma[i][j], sizeof(double), 1, fp);
utils::sfread(FLERR, &k[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &gamma[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&k[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);

19
src/CG-DNA/atom_vec_oxdna.cpp
View File

@ -33,18 +33,13 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "id5p";
fields_copy = (char *) "id5p";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "id5p";
fields_border_vel = (char *) "";
fields_exchange = (char *) "id5p";
fields_restart = (char *) "id5p";
fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_grow = {"id5p"};
fields_copy = {"id5p"};
fields_border = {"id5p"};
fields_exchange = {"id5p"};
fields_restart = {"id5p"};
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();

161
src/DIELECTRIC/atom_vec_dielectric.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
@ -18,23 +17,21 @@
#include "citeme.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_user_dielectric_package[] =
"DIELECTRIC package:\n\n"
"@Article{TrungCPC19,\n"
" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
" Francisco J. Solis, Monica Olvera de la Cruz,\n"
" title = {Incorporating surface polarization effects into large-scale"
" coarse-grained Molecular Dynamics simulation},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2019,\n"
" volume = 241,\n"
" pages = {80--91}\n"
"}\n\n"
;
"DIELECTRIC package:\n\n"
"@Article{TrungCPC19,\n"
" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
" Francisco J. Solis, Monica Olvera de la Cruz,\n"
" title = {Incorporating surface polarization effects into large-scale"
" coarse-grained Molecular Dynamics simulation},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2019,\n"
" volume = 241,\n"
" pages = {80--91}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -54,55 +51,39 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_copy = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_comm = (char *) "q mu area ed em epsilon curvature q_unscaled";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q molecule mu area ed em epsilon curvature q_unscaled";
fields_border_vel = (char *) "q molecule mu area ed em epsilon curvature q_unscaled";
fields_exchange = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special "
"mu area ed em epsilon curvature q_unscaled";
fields_restart = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"mu area ed em epsilon curvature q_unscaled";
fields_create = (char *)
"q molecule num_bond num_angle num_dihedral num_improper nspecial "
"mu area ed em epsilon curvature q_unscaled";
fields_data_atom = (char *) "id molecule type q x "
"mu3 area ed em epsilon curvature";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_copy = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_comm = {"q", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_border = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_border_vel = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature",
"q_unscaled"};
fields_exchange = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
"nspecial", "special", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_restart = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_create = {"q", "molecule", "num_bond", "num_angle", "num_dihedral", "num_improper",
"nspecial", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
fields_data_atom = { "id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon",
"curvature"};
fields_data_vel = {"id v"};
// clang-format on
setup_fields();
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
}
@ -158,13 +139,12 @@ void AtomVecDielectric::data_atom_post(int ilocal)
nspecial[ilocal][1] = 0;
nspecial[ilocal][2] = 0;
double* q = atom->q;
double *q = atom->q;
q_unscaled[ilocal] = q[ilocal];
q[ilocal] /= epsilon[ilocal];
double *mu_one = mu[ilocal];
mu_one[3] =
sqrt(mu_one[0]*mu_one[0] + mu_one[1]*mu_one[1] + mu_one[2]*mu_one[2]);
mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]);
}
/* ----------------------------------------------------------------------
@ -183,14 +163,14 @@ void AtomVecDielectric::unpack_restart_init(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecDielectric::property_atom(char *name)
int AtomVecDielectric::property_atom(const std::string &name)
{
if (strcmp(name,"area") == 0) return 0;
if (strcmp(name,"ed") == 0) return 1;
if (strcmp(name,"em") == 0) return 2;
if (strcmp(name,"epsilon") == 0) return 3;
if (strcmp(name,"curvature") == 0) return 4;
if (strcmp(name,"q_unscaled") == 0) return 5;
if (name == "area") return 0;
if (name == "ed") return 1;
if (name == "em") return 2;
if (name == "epsilon") return 3;
if (name == "curvature") return 4;
if (name == "q_unscaled") return 5;
return -1;
}
@ -199,8 +179,7 @@ int AtomVecDielectric::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecDielectric::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecDielectric::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -208,38 +187,50 @@ void AtomVecDielectric::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = area[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = area[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ed[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ed[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = em[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = em[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = epsilon[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = epsilon[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 4) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = curvature[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = curvature[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 5) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = q_unscaled[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = q_unscaled[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/DIELECTRIC/atom_vec_dielectric.h
View File

@ -35,7 +35,7 @@ class AtomVecDielectric : public AtomVec {
void create_atom_post(int) override;
void data_atom_post(int) override;
void unpack_restart_init(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
protected:

27
src/DIPOLE/atom_vec_dipole.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -34,18 +33,17 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q mu";
fields_copy = (char *) "q mu";
fields_comm = (char *) "mu3";
fields_comm_vel = (char *) "mu3";
fields_reverse = (char *) "";
fields_border = (char *) "q mu";
fields_border_vel = (char *) "q mu";
fields_exchange = (char *) "q mu";
fields_restart = (char *) "q mu";
fields_create = (char *) "q mu";
fields_data_atom = (char *) "id type q x mu3";
fields_data_vel = (char *) "id v";
fields_grow = {"q", "mu"};
fields_copy = {"q", "mu"};
fields_comm = {"mu3"};
fields_comm_vel = {"mu3"};
fields_border = {"q", "mu"};
fields_border_vel = {"q", "mu"};
fields_exchange = {"q", "mu"};
fields_restart = {"q", "mu"};
fields_create = {"q", "mu"};
fields_data_atom = {"id", "type", "q", "x", "mu3"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -68,6 +66,5 @@ void AtomVecDipole::grow_pointers()
void AtomVecDipole::data_atom_post(int ilocal)
{
double *mu_one = mu[ilocal];
mu_one[3] =
sqrt(mu_one[0]*mu_one[0] + mu_one[1]*mu_one[1] + mu_one[2]*mu_one[2]);
mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]);
}

32
src/DPD-MESO/atom_vec_edpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -38,18 +37,18 @@ AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_copy = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_comm = (char *) "edpd_temp vest vest_temp";
fields_comm_vel = (char *) "edpd_temp vest vest_temp";
fields_reverse = (char *) "edpd_flux";
fields_border = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_border_vel = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_exchange = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_restart = (char * ) "edpd_cv edpd_temp vest vest_temp";
fields_create = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_data_atom = (char *) "id type edpd_temp edpd_cv x";
fields_data_vel = (char *) "id v";
fields_grow = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_copy = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_comm = {"edpd_temp", "vest", "vest_temp"};
fields_comm_vel = {"edpd_temp", "vest", "vest_temp"};
fields_reverse = {"edpd_flux"};
fields_border = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_border_vel = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_exchange = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_restart = {"edpd_cv", "edpd_temp", "vest", "vest_temp"};
fields_create = {"edpd_cv", "edpd_temp", "edpd_flux", "vest", "vest_temp"};
fields_data_atom = {"id", "type", "edpd_temp", "edpd_cv", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -60,8 +59,7 @@ void AtomVecEDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style edpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style edpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -85,7 +83,7 @@ void AtomVecEDPD::grow_pointers()
void AtomVecEDPD::force_clear(int n, size_t nbytes)
{
memset(&edpd_flux[n],0,nbytes);
memset(&edpd_flux[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -95,7 +93,7 @@ void AtomVecEDPD::force_clear(int n, size_t nbytes)
void AtomVecEDPD::create_atom_post(int ilocal)
{
edpd_temp[ilocal] = 1.0;
edpd_cv[ilocal]= 1.0e5;
edpd_cv[ilocal] = 1.0e5;
vest_temp[ilocal] = edpd_temp[ilocal];
}

57
src/DPD-MESO/atom_vec_mdpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,10 +12,12 @@
------------------------------------------------------------------------- */
#include "atom_vec_mdpd.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -36,18 +37,18 @@ AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho drho vest";
fields_copy = (char *) "rho drho vest";
fields_comm = (char *) "rho vest";
fields_comm_vel = (char *) "rho vest";
fields_reverse = (char *) "drho";
fields_border = (char *) "rho vest";
fields_border_vel = (char *) "rho vest";
fields_exchange = (char *) "rho vest";
fields_restart = (char * ) "rho vest";
fields_create = (char *) "rho drho vest";
fields_data_atom = (char *) "id type rho x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "drho", "vest"};
fields_copy = {"rho", "drho", "vest"};
fields_comm = {"rho", "vest"};
fields_comm_vel = {"rho", "vest"};
fields_reverse = {"drho"};
fields_border = {"rho", "vest"};
fields_border_vel = {"rho", "vest"};
fields_exchange = {"rho", "vest"};
fields_restart = {"rho", "vest"};
fields_create = {"rho", "drho", "vest"};
fields_data_atom = {"id", "type", "rho", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -58,8 +59,7 @@ void AtomVecMDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style mdpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style mdpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -81,7 +81,7 @@ void AtomVecMDPD::grow_pointers()
void AtomVecMDPD::force_clear(int n, size_t nbytes)
{
memset(&drho[n],0,nbytes);
memset(&drho[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -102,10 +102,10 @@ void AtomVecMDPD::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecMDPD::property_atom(char *name)
int AtomVecMDPD::property_atom(const std::string &name)
{
if (strcmp(name,"rho") == 0) return 0;
if (strcmp(name,"drho") == 0) return 1;
if (name == "rho") return 0;
if (name == "drho") return 1;
return -1;
}
@ -114,8 +114,7 @@ int AtomVecMDPD::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecMDPD::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecMDPD::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -123,14 +122,18 @@ void AtomVecMDPD::pack_property_atom(int index, double *buf,
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = rho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = drho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = drho[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/DPD-MESO/atom_vec_mdpd.h
View File

@ -32,7 +32,7 @@ class AtomVecMDPD : public AtomVec {
void grow_pointers() override;
void force_clear(int, size_t) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

48
src/DPD-MESO/atom_vec_tdpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -13,11 +12,12 @@
------------------------------------------------------------------------- */
#include "atom_vec_tdpd.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "error.h"
#include "atom.h"
#include "error.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
@ -37,18 +37,18 @@ AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "cc cc_flux vest";
fields_copy = (char *) "cc vest";
fields_comm = (char *) "cc vest";
fields_comm_vel = (char *) "cc vest";
fields_reverse = (char *) "cc_flux";
fields_border = (char *) "cc vest";
fields_border_vel = (char *) "cc vest";
fields_exchange = (char *) "cc vest";
fields_restart = (char * ) "cc vest";
fields_create = (char *) "cc vest";
fields_data_atom = (char *) "id type x cc";
fields_data_vel = (char *) "id v";
fields_grow = {"cc", "cc_flux", "vest"};
fields_copy = {"cc", "vest"};
fields_comm = {"cc", "vest"};
fields_comm_vel = {"cc", "vest"};
fields_reverse = {"cc_flux"};
fields_border = {"cc", "vest"};
fields_border_vel = {"cc", "vest"};
fields_exchange = {"cc", "vest"};
fields_restart = {"cc", "vest"};
fields_create = {"cc", "vest"};
fields_data_atom = {"id", "type", "x", "cc"};
fields_data_vel = {"id", "v"};
}
/* ----------------------------------------------------------------------
@ -58,13 +58,13 @@ AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecTDPD::process_args(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Invalid atom_style tdpd command");
if (narg < 1) error->all(FLERR, "Invalid atom_style tdpd command");
atom->cc_species = utils::inumeric(FLERR,arg[0],false,lmp);
atom->cc_species = utils::inumeric(FLERR, arg[0], false, lmp);
cc_species = atom->cc_species;
atom->add_peratom_change_columns("cc",cc_species);
atom->add_peratom_change_columns("cc_flux",cc_species);
atom->add_peratom_change_columns("cc", cc_species);
atom->add_peratom_change_columns("cc_flux", cc_species);
// delay setting up of fields until now
@ -77,8 +77,7 @@ void AtomVecTDPD::init()
{
AtomVec::init();
if (strcmp(update->unit_style,"lj") != 0)
error->all(FLERR,"Atom style tdpd requires lj units");
if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style tdpd requires lj units");
}
/* ----------------------------------------------------------------------
@ -92,7 +91,6 @@ void AtomVecTDPD::grow_pointers()
vest = atom->vest;
}
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
@ -100,7 +98,7 @@ void AtomVecTDPD::grow_pointers()
void AtomVecTDPD::force_clear(int n, size_t nbytes)
{
memset(&cc_flux[n][0],0,cc_species*nbytes);
memset(&cc_flux[n][0], 0, cc_species * nbytes);
}
/* ----------------------------------------------------------------------

28
src/DPD-REACT/atom_vec_dpd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -17,6 +16,7 @@
------------------------------------------------------------------------- */
#include "atom_vec_dpd.h"
#include "atom.h"
#include "error.h"
@ -37,18 +37,17 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho dpdTheta uCond uMech uChem uCG uCGnew duChem";
fields_copy = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_comm = (char *) "dpdTheta uCond uMech uChem";
fields_comm_vel = (char *) "dpdTheta uCond uMech uChem";
fields_reverse = (char *) "";
fields_border = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_border_vel = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_exchange = (char *) "dpdTheta uCond uMech uChem uCG uCGnew";
fields_restart = (char *) "dpdTheta uCond uMech uChem";
fields_create = (char *) "rho dpdTheta uCond uMech uChem uCG uCGnew duChem";
fields_data_atom = (char *) "id type dpdTheta x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew", "duChem"};
fields_copy = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_comm = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_comm_vel = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_border = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_border_vel = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_exchange = {"dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew"};
fields_restart = {"dpdTheta", "uCond", "uMech", "uChem"};
fields_create = {"rho", "dpdTheta", "uCond", "uMech", "uChem", "uCG", "uCGnew", "duChem"};
fields_data_atom = {"id", "type", "dpdTheta", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -94,6 +93,5 @@ void AtomVecDPD::data_atom_post(int ilocal)
uCGnew[ilocal] = 0.0;
if (dpdTheta[ilocal] <= 0)
error->one(FLERR,"Internal temperature in Atoms section of date file "
"must be > zero");
error->one(FLERR, "Internal temperature in Atoms section of date file must be > zero");
}

88
src/EFF/atom_vec_electron.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -21,20 +20,19 @@
#include "atom.h"
#include "citeme.h"
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_user_eff_package[] =
"EFF package:\n\n"
"@Article{Jaramillo-Botero11,\n"
" author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
" title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},\n"
" journal = {J.~Comp.~Chem.},\n"
" year = 2011,\n"
" volume = 32,\n"
" pages = {497--512}\n"
"}\n\n";
"EFF package:\n\n"
"@Article{Jaramillo-Botero11,\n"
" author = {A. Jaramillo-Botero, J. Su, A. Qi, W. A. Goddard III},\n"
" title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing "
"Material Properties and Phenomena in Extreme Environments},\n"
" journal = {J.~Comp.~Chem.},\n"
" year = 2011,\n"
" volume = 32,\n"
" pages = {497--512}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -47,26 +45,25 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
forceclearflag = 1;
atom->electron_flag = 1;
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->q_flag = atom->spin_flag = atom->eradius_flag = atom->ervel_flag = atom->erforce_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q spin eradius ervel erforce";
fields_copy = (char *) "q spin eradius ervel";
fields_comm = (char *) "eradius";
fields_comm_vel = (char *) "eradius";
fields_reverse = (char *) "erforce";
fields_border = (char *) "q spin eradius";
fields_border_vel = (char *) "q spin eradius";
fields_exchange = (char *) "q spin eradius ervel";
fields_restart = (char *) "q spin eradius ervel";
fields_create = (char *) "q spin eradius ervel";
fields_data_atom = (char *) "id type q spin eradius x";
fields_data_vel = (char *) "id v ervel";
fields_grow = {"q", "spin", "eradius", "ervel", "erforce"};
fields_copy = {"q", "spin", "eradius", "ervel"};
fields_comm = {"eradius"};
fields_comm_vel = {"eradius"};
fields_reverse = {"erforce"};
fields_border = {"q", "spin", "eradius"};
fields_border_vel = {"q", "spin", "eradius"};
fields_exchange = {"q", "spin", "eradius", "ervel"};
fields_restart = {"q", "spin", "eradius", "ervel"};
fields_create = {"q", "spin", "eradius", "ervel"};
fields_data_atom = {"id", "type", "q", "spin", "eradius", "x"};
fields_data_vel = {"id", "v", "ervel"};
setup_fields();
}
@ -91,7 +88,7 @@ void AtomVecElectron::grow_pointers()
void AtomVecElectron::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
memset(&erforce[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -119,12 +116,12 @@ void AtomVecElectron::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecElectron::property_atom(char *name)
int AtomVecElectron::property_atom(const std::string &name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
if (name == "spin") return 0;
if (name == "eradius") return 1;
if (name == "ervel") return 2;
if (name == "erforce") return 3;
return -1;
}
@ -133,8 +130,7 @@ int AtomVecElectron::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecElectron::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecElectron::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -142,26 +138,34 @@ void AtomVecElectron::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = spin[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = eradius[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = ervel[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = erforce[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/EFF/atom_vec_electron.h
View File

@ -32,7 +32,7 @@ class AtomVecElectron : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

2
src/EXTRA-COMPUTE/compute_born_matrix.cpp
View File

@ -586,7 +586,7 @@ void ComputeBornMatrix::restore_atoms(int nall, int idir)
int k = dirlist[idir][0];
int l = dirlist[idir][1];
double **x = atom->x;
if (l == k)
if (l == k)
for (int i = 0; i < nall; i++) x[i][k] = temp_x[i][k];
else
for (int i = 0; i < nall; i++) {

2
src/EXTRA-MOLECULE/bond_fene_nm.cpp
View File

@ -273,7 +273,7 @@ double BondFENENM::single(int type, double rsq, int /*i*/, int /*j*/, double &ff
void *BondFENENM::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "kappa") == 0) return (void *) k;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}

4
src/EXTRA-MOLECULE/bond_gaussian.cpp
View File

@ -34,9 +34,7 @@ using namespace MathConst;
BondGaussian::BondGaussian(LAMMPS *lmp) :
Bond(lmp), nterms(nullptr), bond_temperature(nullptr), alpha(nullptr), width(nullptr),
r0(nullptr)
{
reinitflag = 1;
}
{}
/* ---------------------------------------------------------------------- */

95
src/EXTRA-PAIR/pair_coul_slater_long.cpp
View File

@ -45,7 +45,6 @@ using namespace LAMMPS_NS;
PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
//ftable = nullptr;
qdist = 0.0;
}
@ -117,7 +116,6 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
@ -127,22 +125,6 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = scale[itype][jtype] * qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
fpair = forcecoul * r2inv;
@ -156,14 +138,7 @@ void PairCoulSlaterLong::compute(int eflag, int vflag)
}
if (eflag) {
// if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
ecoul = scale[itype][jtype] * qtmp*q[j] * table;
}
*/
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
}
@ -296,10 +271,10 @@ void PairCoulSlaterLong::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) fread(&scale[i][j],sizeof(double),1,fp);
if (me == 0) utils::sfread(FLERR, &scale[i][j],sizeof(double),1,fp, nullptr, error);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
@ -315,8 +290,6 @@ void PairCoulSlaterLong::write_restart_settings(FILE *fp)
fwrite(&lamda,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
//fwrite(&ncoultablebits,sizeof(int),1,fp);
//fwrite(&tabinner,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
@ -326,71 +299,39 @@ void PairCoulSlaterLong::write_restart_settings(FILE *fp)
void PairCoulSlaterLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_coul,sizeof(double),1,fp);
fread(&lamda,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
//fread(&ncoultablebits,sizeof(int),1,fp);
//fread(&tabinner,sizeof(double),1,fp);
utils::sfread(FLERR, &cut_coul,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &lamda,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
//MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
//MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
double PairCoulSlaterLong::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
double factor_coul, double /*factor_lj*/,
double &fforce)
double PairCoulSlaterLong::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
double factor_coul, double /*factor_lj*/, double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double slater_term;
// double fraction,table;
double forcecoul,phicoul;
// int itable;
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
fforce = forcecoul * r2inv;
// if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
*/
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
return phicoul;

1
src/EXTRA-PAIR/pair_coul_slater_long.h
View File

@ -43,7 +43,6 @@ class PairCoulSlaterLong : public Pair {
protected:
double cut_coul, cut_coulsq, qdist;
double lamda;
//double *cut_respa;
double g_ewald;
double **scale;

18
src/EXTRA-PAIR/pair_wf_cut.cpp
View File

@ -294,15 +294,15 @@ void PairWFCut::read_restart(FILE *fp)
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
if (me == 0) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&nu[i][j],sizeof(int),1,fp);
fread(&mu[i][j],sizeof(int),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
utils::sfread(FLERR, &epsilon[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &sigma[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &nu[i][j],sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &mu[i][j],sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j],sizeof(double),1,fp, nullptr, error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
@ -331,9 +331,9 @@ void PairWFCut::write_restart_settings(FILE *fp)
void PairWFCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
utils::sfread(FLERR, &cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);

2
src/INTEL/verlet_lrt_intel.cpp
View File

@ -215,7 +215,7 @@ void VerletLRTIntel::run(int n)
int n_pre_neighbor = modify->n_pre_neighbor;
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
int n_end_of_step = modify->n_end_of_step;
if (atom->sortfreq > 0) sortflag = 1;

17
src/KOKKOS/atom_vec_hybrid_kokkos.cpp
View File

@ -1073,17 +1073,14 @@ void AtomVecHybridKokkos::write_data(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4]);
fmt::print(fp,"{} {} {:.16e} {:.16e} {:.16e}", ubuf(buf[i][0]).i, ubuf(buf[i][1]).i,
buf[i][2], buf[i][3], buf[i][4]);
m = 5;
for (k = 0; k < nstyles; k++)
m += styles[k]->write_data_hybrid(fp,&buf[i][m]);
fprintf(fp," %d %d %d\n",
(int) ubuf(buf[i][m]).i,(int) ubuf(buf[i][m+1]).i,
(int) ubuf(buf[i][m+2]).i);
fmt::print(fp," {} {} {}\n", ubuf(buf[i][m]).i, ubuf(buf[i][m+1]).i, ubuf(buf[i][m+2]).i);
}
}
@ -1119,8 +1116,7 @@ void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT " %g %g %g",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
fmt::print(fp,"{} {} {} {}", (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
m = 4;
for (k = 0; k < nstyles; k++)
@ -1136,7 +1132,7 @@ void AtomVecHybridKokkos::write_vel(FILE *fp, int n, double **buf)
return -1 if name is unknown to any sub-styles
------------------------------------------------------------------------- */
int AtomVecHybridKokkos::property_atom(char *name)
int AtomVecHybridKokkos::property_atom(const std::string &name)
{
for (int k = 0; k < nstyles; k++) {
int index = styles[k]->property_atom(name);
@ -1150,8 +1146,7 @@ int AtomVecHybridKokkos::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
void AtomVecHybridKokkos::pack_property_atom(int multiindex, double *buf, int nvalues, int groupbit)
{
int k = multiindex % nstyles;
int index = multiindex/nstyles;

2
src/KOKKOS/atom_vec_hybrid_kokkos.h
View File

@ -64,7 +64,7 @@ class AtomVecHybridKokkos : public AtomVecKokkos {
void write_data(FILE *, int, double **) override;
void pack_vel(double **) override;
void write_vel(FILE *, int, double **) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
double memory_usage() override;

2
src/KOKKOS/dynamical_matrix_kokkos.cpp
View File

@ -159,7 +159,7 @@ void DynamicalMatrixKokkos::update_force()
{
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
lmp->kokkos->auto_sync = 0;

2
src/KOKKOS/third_order_kokkos.cpp
View File

@ -160,7 +160,7 @@ void ThirdOrderKokkos::update_force()
{
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
lmp->kokkos->auto_sync = 0;

2
src/KOKKOS/verlet_kokkos.cpp
View File

@ -271,7 +271,7 @@ void VerletKokkos::run(int n)
int n_post_neighbor = modify->n_post_neighbor;
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
int n_end_of_step = modify->n_end_of_step;
lmp->kokkos->auto_sync = 0;

80
src/MACHDYN/atom_vec_smd.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
@ -27,8 +26,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
#define NMAT_FULL 9
@ -63,42 +60,33 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"esph desph vfrac rmass x0 radius contact_radius molecule "
"smd_data_9 vest smd_stress "
"eff_plastic_strain eff_plastic_strain_rate damage";
fields_copy = (char *)
"esph vfrac rmass x0 radius contact_radius molecule "
"eff_plastic_strain eff_plastic_strain_rate vest "
"smd_data_9 smd_stress damage";
fields_comm = (char *) "radius vfrac vest esph";
fields_comm_vel = (char *) "radius vfrac vest esph";
fields_reverse = (char *) "desph";
fields_border = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain smd_data_9 smd_stress";
fields_border_vel = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain smd_data_9 smd_stress vest";
fields_exchange = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress "
"vest damage";
fields_restart = (char *)
"x0 molecule radius rmass vfrac contact_radius esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress "
"vest damage";
fields_create = (char *)
"x0 vest vfrac rmass radius contact_radius molecule esph "
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress damage";
fields_data_atom = (char *)
"id type molecule vfrac rmass radius contact_radius x0 x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"esph", "desph", "vfrac", "rmass", "x0", "radius", "contact_radius", "molecule",
"smd_data_9", "vest", "smd_stress", "eff_plastic_strain", "eff_plastic_strain_rate", "damage"};
fields_copy = {"esph", "vfrac", "rmass", "x0", "radius", "contact_radius", "molecule",
"eff_plastic_strain", "eff_plastic_strain_rate", "vest", "smd_data_9", "smd_stress", "damage"};
fields_comm = {"radius", "vfrac", "vest", "esph"};
fields_comm_vel = {"radius", "vfrac", "vest", "esph"};
fields_reverse = {"desph"};
fields_border = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "smd_data_9", "smd_stress"};
fields_border_vel = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "smd_data_9", "smd_stress", "vest"};
fields_exchange = {"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "vest", "damage"};
fields_restart ={"x0", "molecule", "radius", "rmass", "vfrac", "contact_radius", "esph",
"eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "vest", "damage"};
fields_create = {"x0", "vest", "vfrac", "rmass", "radius", "contact_radius", "molecule",
"esph", "eff_plastic_strain", "eff_plastic_strain_rate", "smd_data_9", "smd_stress", "damage"};
fields_data_atom = {"id", "type", "molecule", "vfrac", "rmass", "radius", "contact_radius",
"x0", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
// set these array sizes based on defines
atom->add_peratom_change_columns("smd_data_9",NMAT_FULL);
atom->add_peratom_change_columns("smd_stress",NMAT_SYMM);
atom->add_peratom_change_columns("smd_data_9", NMAT_FULL);
atom->add_peratom_change_columns("smd_stress", NMAT_SYMM);
setup_fields();
}
@ -134,7 +122,7 @@ void AtomVecSMD::grow_pointers()
void AtomVecSMD::force_clear(int n, size_t nbytes)
{
memset(&desph[n],0,nbytes);
memset(&desph[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -153,9 +141,9 @@ void AtomVecSMD::create_atom_post(int ilocal)
contact_radius[ilocal] = 0.5;
molecule[ilocal] = 1;
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
}
/* ----------------------------------------------------------------------
@ -179,13 +167,11 @@ void AtomVecSMD::data_atom_post(int ilocal)
eff_plastic_strain[ilocal] = 0.0;
eff_plastic_strain_rate[ilocal] = 0.0;
for (int k = 0; k < NMAT_FULL; k++)
smd_data_9[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_FULL; k++) smd_data_9[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_SYMM; k++)
smd_stress[ilocal][k] = 0.0;
for (int k = 0; k < NMAT_SYMM; k++) smd_stress[ilocal][k] = 0.0;
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
smd_data_9[ilocal][0] = 1.0; // xx
smd_data_9[ilocal][4] = 1.0; // yy
smd_data_9[ilocal][8] = 1.0; // zz
}

2
src/MAKE/MACHINES/Makefile.summit_kokkos
View File

@ -9,7 +9,7 @@ SHELL = /bin/sh
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
CC = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
CCFLAGS = -g -O3 -DNDEBUG
CCFLAGS = -g -O3 -DNDEBUG -Xcudafe --diag_suppress=unrecognized_pragma
SHFLAGS = -fPIC
DEPFLAGS = -M

4
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
View File

@ -10,7 +10,7 @@ KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
CC = mpicxx
CCFLAGS = -g -O3 -DNDEBUG
CCFLAGS = -g -O3 -DNDEBUG -Xcudafe --diag_suppress=unrecognized_pragma
SHFLAGS = -fPIC
DEPFLAGS = -M
@ -55,7 +55,7 @@ MPI_LIB =
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -DFFT_CUFFT
FFT_INC = -DFFT_CUFFT
FFT_PATH =
FFT_LIB = -lcufft

2
src/MC/fix_atom_swap.cpp
View File

@ -532,7 +532,7 @@ double FixAtomSwap::energy_full()
if (force->kspace) force->kspace->compute(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_post_force_any) modify->post_force(vflag);
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();

2
src/MC/fix_charge_regulation.cpp
View File

@ -1129,7 +1129,7 @@ double FixChargeRegulation::energy_full() {
if (force->kspace) force->kspace->compute(eflag, vflag);
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_post_force_any) modify->post_force(vflag);
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();

2
src/MC/fix_gcmc.cpp
View File

@ -2316,7 +2316,7 @@ double FixGCMC::energy_full()
// but Modify::pre_reverse() is needed for INTEL
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_post_force_any) modify->post_force(vflag);
// NOTE: all fixes with energy_global_flag set and which
// operate at pre_force() or post_force()

2
src/MC/fix_mol_swap.cpp
View File

@ -390,7 +390,7 @@ double FixMolSwap::energy_full()
if (force->kspace) force->kspace->compute(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_post_force_any) modify->post_force(vflag);
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();

23
src/MESONT/atom_vec_mesont.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -33,18 +32,16 @@ AtomVecMesoNT::AtomVecMesoNT(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass radius length buckling bond_nt molecule";
fields_copy = (char *) "rmass radius length buckling bond_nt molecule";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "rmass radius length buckling bond_nt molecule";
fields_border_vel = (char *) "rmass radius length buckling bond_nt molecule";
fields_exchange = (char *) "rmass radius length buckling bond_nt molecule";
fields_restart = (char *) "rmass radius length buckling bond_nt molecule";
fields_create = (char *) "rmass radius length buckling bond_nt molecule";
fields_data_atom = (char *) "id molecule type bond_nt rmass radius length buckling x";
fields_data_vel = (char *) "id v";
fields_grow = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_copy = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_border = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_border_vel = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_exchange = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_restart = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_create = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
fields_data_atom = {"id", "molecule", "type", "bond_nt", "rmass",
"radius", "length", "buckling", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

1
src/ML-SNAP/pair_snap.cpp
View File

@ -703,7 +703,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (keywd == "rinner") {
keyval = words[iword];
for (int ielem = 0; ielem < nelements; ielem++) {
printf("rinnerelem = %p ielem = %d nelements = %d iword = %d nwords = %d\n",rinnerelem, ielem, nelements, iword, nwords);
rinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp);
iword++;
}

11
src/MOLECULE/angle_cosine.cpp
View File

@ -237,10 +237,21 @@ double AngleCosine::single(int type, int i1, int i2, int i3)
return k[type] * (1.0 + c);
}
/* ---------------------------------------------------------------------- */
void AngleCosine::born_matrix(int type, int i1, int i2, int i3, double& du, double& du2)
{
du2 = 0;
du = k[type];
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleCosine::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k") == 0) return (void *) k;
return nullptr;
}

1
src/MOLECULE/angle_cosine.h
View File

@ -36,6 +36,7 @@ class AngleCosine : public Angle {
void write_data(FILE *) override;
double single(int, int, int, int) override;
void born_matrix(int type, int i1, int i2, int i3, double& du, double& du2) override;
void *extract(const char *, int &) override;
protected:
double *k;

12
src/MOLECULE/angle_harmonic.cpp
View File

@ -264,3 +264,15 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3)
double tk = k[type] * dtheta;
return tk * dtheta;
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleHarmonic::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/MOLECULE/angle_harmonic.h
View File

@ -35,6 +35,7 @@ class AngleHarmonic : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
double *k, *theta0;

51
src/MOLECULE/atom_vec_angle.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,26 +31,22 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 nspecial special";
fields_restart = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3";
fields_create = (char *) "molecule num_bond num_angle nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2",
"angle_atom3", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3"};
fields_create = {"molecule", "num_bond", "num_angle", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
@ -63,8 +58,8 @@ AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp)
AtomVecAngle::~AtomVecAngle()
{
delete [] bond_negative;
delete [] angle_negative;
delete[] bond_negative;
delete[] angle_negative;
}
/* ----------------------------------------------------------------------
@ -90,12 +85,12 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
@ -108,7 +103,8 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -117,7 +113,8 @@ void AtomVecAngle::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
}

32
src/MOLECULE/atom_vec_bond.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,21 +31,15 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom nspecial special";
fields_restart = (char *) "molecule num_bond bond_type bond_atom";
fields_create = (char *) "molecule num_bond nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom"};
fields_create = {"molecule", "num_bond", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
@ -58,7 +51,7 @@ AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
AtomVecBond::~AtomVecBond()
{
delete [] bond_negative;
delete[] bond_negative;
}
/* ----------------------------------------------------------------------
@ -82,7 +75,7 @@ void AtomVecBond::pack_restart_pre(int ilocal)
// insure bond_negative vector is needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
@ -95,7 +88,8 @@ void AtomVecBond::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
}

101
src/MOLECULE/atom_vec_full.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,47 +31,31 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_copy = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q molecule";
fields_border_vel = (char *) "q molecule";
fields_exchange = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_restart = (char *)
"q molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4";
fields_create = (char *)
"q molecule num_bond num_angle num_dihedral num_improper nspecial";
fields_data_atom = (char *) "id molecule type q x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_copy = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_border = {"q", "molecule"};
fields_border_vel = {"q", "molecule"};
fields_exchange = {"q", "molecule", "num_bond", "bond_type", "bond_atom",
"num_angle", "angle_type", "angle_atom1", "angle_atom2", "angle_atom3",
"num_dihedral", "dihedral_type", "dihedral_atom1", "dihedral_atom2",
"dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type", "improper_atom1",
"improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_restart = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4"};
fields_create = {"q", "molecule", "num_bond", "num_angle",
"num_dihedral", "num_improper", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "q", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
setup_fields();
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
@ -83,10 +66,10 @@ AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
AtomVecFull::~AtomVecFull()
{
delete [] bond_negative;
delete [] angle_negative;
delete [] dihedral_negative;
delete [] improper_negative;
delete[] bond_negative;
delete[] angle_negative;
delete[] dihedral_negative;
delete[] improper_negative;
}
/* ----------------------------------------------------------------------
@ -116,22 +99,22 @@ void AtomVecFull::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
if (dihedral_per_atom < atom->dihedral_per_atom) {
delete [] dihedral_negative;
delete[] dihedral_negative;
dihedral_per_atom = atom->dihedral_per_atom;
dihedral_negative = new int[dihedral_per_atom];
}
if (improper_per_atom < atom->improper_per_atom) {
delete [] improper_negative;
delete[] improper_negative;
improper_per_atom = atom->improper_per_atom;
improper_negative = new int[improper_per_atom];
}
@ -144,7 +127,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -153,7 +137,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
any_dihedral_negative = 0;
@ -162,7 +147,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
dihedral_negative[m] = 1;
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
any_dihedral_negative = 1;
} else dihedral_negative[m] = 0;
} else
dihedral_negative[m] = 0;
}
any_improper_negative = 0;
@ -171,7 +157,8 @@ void AtomVecFull::pack_restart_pre(int ilocal)
improper_negative[m] = 1;
improper_type[ilocal][m] = -improper_type[ilocal][m];
any_improper_negative = 1;
} else improper_negative[m] = 0;
} else
improper_negative[m] = 0;
}
}
@ -195,14 +182,12 @@ void AtomVecFull::pack_restart_post(int ilocal)
if (any_dihedral_negative) {
for (int m = 0; m < num_dihedral[ilocal]; m++)
if (dihedral_negative[m])
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
if (dihedral_negative[m]) dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
}
if (any_improper_negative) {
for (int m = 0; m < num_improper[ilocal]; m++)
if (improper_negative[m])
improper_type[ilocal][m] = -improper_type[ilocal][m];
if (improper_negative[m]) improper_type[ilocal][m] = -improper_type[ilocal][m];
}
}

98
src/MOLECULE/atom_vec_molecular.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -32,46 +31,29 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_copy = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule";
fields_border_vel = (char *) "molecule";
fields_exchange = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4 "
"nspecial special";
fields_restart = (char *)
"molecule num_bond bond_type bond_atom "
"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
"dihedral_atom3 dihedral_atom4 "
"num_improper improper_type improper_atom1 improper_atom2 "
"improper_atom3 improper_atom4";
fields_create = (char *)
"molecule num_bond num_angle num_dihedral num_improper nspecial";
fields_data_atom = (char *) "id molecule type x";
fields_data_vel = (char *) "id v";
// clang-format off
fields_grow = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_copy = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_border = {"molecule"};
fields_border_vel = {"molecule"};
fields_exchange = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special"};
fields_restart = {"molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4"};
fields_create = {"molecule", "num_bond", "num_angle", "num_dihedral", "num_improper", "nspecial"};
fields_data_atom = {"id", "molecule", "type", "x"};
fields_data_vel = {"id", "v"};
// clang-format on
setup_fields();
@ -83,10 +65,10 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp)
AtomVecMolecular::~AtomVecMolecular()
{
delete [] bond_negative;
delete [] angle_negative;
delete [] dihedral_negative;
delete [] improper_negative;
delete[] bond_negative;
delete[] angle_negative;
delete[] dihedral_negative;
delete[] improper_negative;
}
/* ----------------------------------------------------------------------
@ -116,22 +98,22 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
// insure negative vectors are needed length
if (bond_per_atom < atom->bond_per_atom) {
delete [] bond_negative;
delete[] bond_negative;
bond_per_atom = atom->bond_per_atom;
bond_negative = new int[bond_per_atom];
}
if (angle_per_atom < atom->angle_per_atom) {
delete [] angle_negative;
delete[] angle_negative;
angle_per_atom = atom->angle_per_atom;
angle_negative = new int[angle_per_atom];
}
if (dihedral_per_atom < atom->dihedral_per_atom) {
delete [] dihedral_negative;
delete[] dihedral_negative;
dihedral_per_atom = atom->dihedral_per_atom;
dihedral_negative = new int[dihedral_per_atom];
}
if (improper_per_atom < atom->improper_per_atom) {
delete [] improper_negative;
delete[] improper_negative;
improper_per_atom = atom->improper_per_atom;
improper_negative = new int[improper_per_atom];
}
@ -144,7 +126,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
bond_negative[m] = 1;
bond_type[ilocal][m] = -bond_type[ilocal][m];
any_bond_negative = 1;
} else bond_negative[m] = 0;
} else
bond_negative[m] = 0;
}
any_angle_negative = 0;
@ -153,7 +136,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
angle_negative[m] = 1;
angle_type[ilocal][m] = -angle_type[ilocal][m];
any_angle_negative = 1;
} else angle_negative[m] = 0;
} else
angle_negative[m] = 0;
}
any_dihedral_negative = 0;
@ -162,7 +146,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
dihedral_negative[m] = 1;
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
any_dihedral_negative = 1;
} else dihedral_negative[m] = 0;
} else
dihedral_negative[m] = 0;
}
any_improper_negative = 0;
@ -171,7 +156,8 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
improper_negative[m] = 1;
improper_type[ilocal][m] = -improper_type[ilocal][m];
any_improper_negative = 1;
} else improper_negative[m] = 0;
} else
improper_negative[m] = 0;
}
}
@ -195,14 +181,12 @@ void AtomVecMolecular::pack_restart_post(int ilocal)
if (any_dihedral_negative) {
for (int m = 0; m < num_dihedral[ilocal]; m++)
if (dihedral_negative[m])
dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
if (dihedral_negative[m]) dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
}
if (any_improper_negative) {
for (int m = 0; m < num_improper[ilocal]; m++)
if (improper_negative[m])
improper_type[ilocal][m] = -improper_type[ilocal][m];
if (improper_negative[m]) improper_type[ilocal][m] = -improper_type[ilocal][m];
}
}

40
src/MOLECULE/atom_vec_template.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -36,18 +35,15 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in the string does not matter
// except fields_data_atom and fields_data_vel which must match data file
fields_grow = (char *) "molecule molindex molatom";
fields_copy = (char *) "molecule molindex molatom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "molecule molindex molatom";
fields_border_vel = (char *) "molecule molindex molatom";
fields_exchange = (char *) "molecule molindex molatom";
fields_restart = (char *) "molecule molindex molatom";
fields_create = (char *) "molecule molindex molatom";
fields_data_atom = (char *) "id molecule molindex molatom type x";
fields_data_vel = (char *) "id v";
fields_grow = {"molecule", "molindex", "molatom"};
fields_copy = {"molecule", "molindex", "molatom"};
fields_border = {"molecule", "molindex", "molatom"};
fields_border_vel = {"molecule", "molindex", "molatom"};
fields_exchange = {"molecule", "molindex", "molatom"};
fields_restart = {"molecule", "molindex", "molatom"};
fields_create = {"molecule", "molindex", "molatom"};
fields_data_atom = {"id", "molecule", "molindex", "molatom", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -58,11 +54,10 @@ AtomVecTemplate::AtomVecTemplate(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecTemplate::process_args(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal atom_style template command");
if (narg != 1) error->all(FLERR, "Illegal atom_style template command");
int imol = atom->find_molecule(arg[0]);
if (imol == -1) error->all(FLERR,"Molecule template ID for "
"atom_style template does not exist");
if (imol == -1) error->all(FLERR, "Molecule template ID for atom_style template does not exist");
onemols = &atom->molecules[imol];
nset = atom->molecules[imol]->nset;
@ -81,10 +76,10 @@ void AtomVecTemplate::process_args(int narg, char **arg)
// do this here b/c data file will typically not contain these settings
for (int i = 0; i < nset; i++) {
atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes);
atom->nangletypes = MAX(atom->nangletypes,onemols[i]->nangletypes);
atom->ndihedraltypes = MAX(atom->ndihedraltypes,onemols[i]->ndihedraltypes);
atom->nimpropertypes = MAX(atom->nimpropertypes,onemols[i]->nimpropertypes);
atom->nbondtypes = MAX(atom->nbondtypes, onemols[i]->nbondtypes);
atom->nangletypes = MAX(atom->nangletypes, onemols[i]->nangletypes);
atom->ndihedraltypes = MAX(atom->ndihedraltypes, onemols[i]->ndihedraltypes);
atom->nimpropertypes = MAX(atom->nimpropertypes, onemols[i]->nimpropertypes);
}
}
@ -129,7 +124,6 @@ void AtomVecTemplate::pack_data_post(int ilocal)
molatom[ilocal]--;
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
@ -141,7 +135,7 @@ void AtomVecTemplate::data_atom_post(int ilocal)
int molatom_one = --molatom[ilocal];
if ((molindex_one < -1) || (molindex_one >= nset))
error->one(FLERR,"Invalid template index in Atoms section of data file");
error->one(FLERR, "Invalid template index in Atoms section of data file");
if ((molatom_one < -1) || ((molindex_one >= 0) && (molatom_one >= onemols[molindex_one]->natoms)))
error->one(FLERR,"Invalid template atom in Atoms section of data file");
error->one(FLERR, "Invalid template atom in Atoms section of data file");
}

2
src/MOLECULE/bond_fene.cpp
View File

@ -265,7 +265,7 @@ double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/, double &ffor
void *BondFENE::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "kappa") == 0) return (void *) k;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}

7
src/MOLECULE/bond_gromos.cpp
View File

@ -30,10 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondGromos::BondGromos(LAMMPS *_lmp) : Bond(_lmp)
{
reinitflag = 1;
}
BondGromos::BondGromos(LAMMPS *_lmp) : Bond(_lmp) {}
/* ---------------------------------------------------------------------- */
@ -200,7 +197,7 @@ double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/, double &ff
void *BondGromos::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "kappa") == 0) return (void *) k;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}

6
src/MOLECULE/bond_harmonic.cpp
View File

@ -29,7 +29,6 @@ using namespace LAMMPS_NS;
BondHarmonic::BondHarmonic(LAMMPS *_lmp) : Bond(_lmp)
{
reinitflag = 1;
born_matrix_enable = 1;
}
@ -216,12 +215,13 @@ void BondHarmonic::born_matrix(int type, double rsq, int /*i*/, int /*j*/,
}
/* ----------------------------------------------------------------------
Return ptr to internal members upon request.
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *BondHarmonic::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "kappa") == 0) return (void *) k;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}

4
src/OPENMP/respa_omp.cpp
View File

@ -77,7 +77,7 @@ void RespaOMP::setup(int flag)
mesg += fmt::format(" {}:{}", ilevel + 1, step[ilevel]);
mesg += "\n r-RESPA fixes :";
for (int l = 0; l < modify->n_post_force_respa; ++l) {
for (int l = 0; l < modify->n_post_force_respa_any; ++l) {
Fix *f = modify->get_fix_by_index(modify->list_post_force_respa[l]);
if (f->respa_level >= 0)
mesg += fmt::format(" {}:{}[{}]", MIN(f->respa_level + 1, nlevels), f->style, f->id);
@ -420,7 +420,7 @@ void RespaOMP::recurse(int ilevel)
timer->stamp(Timer::COMM);
}
timer->stamp();
if (modify->n_post_force_respa)
if (modify->n_post_force_respa_any)
modify->post_force_respa(vflag,ilevel,iloop);
modify->final_integrate_respa(ilevel,iloop);
timer->stamp(Timer::MODIFY);

67
src/PERI/atom_vec_peri.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,20 +22,19 @@
#include "error.h"
#include <cfloat>
#include <cstring>
using namespace LAMMPS_NS;
static const char cite_peri_package[] =
"PERI package for Peridynamics:\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {777--783}\n"
"}\n\n";
"PERI package for Peridynamics:\n\n"
"@Article{Parks08,\n"
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
" title = {Implementing peridynamics within a molecular dynamics code},\n"
" journal = {Comp.~Phys.~Comm.},\n"
" year = 2008,\n"
" volume = 179,\n"
" pages = {777--783}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -55,18 +53,17 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass vfrac s0 x0";
fields_copy = (char *) "rmass vfrac s0 x0";
fields_comm = (char *) "s0";
fields_comm_vel = (char *) "s0";
fields_reverse = (char *) "";
fields_border = (char *) "rmass vfrac s0 x0";
fields_border_vel = (char *) "rmass vfrac s0 x0";
fields_exchange = (char *) "rmass vfrac s0 x0";
fields_restart = (char *) "rmass vfrac s0 x0";
fields_create = (char *) "rmass vfrac s0 x0";
fields_data_atom = (char *) "id type vfrac rmass x";
fields_data_vel = (char *) "id v";
fields_grow = {"rmass", "vfrac", "s0", "x0"};
fields_copy = {"rmass", "vfrac", "s0", "x0"};
fields_comm = {"s0"};
fields_comm_vel = {"s0"};
fields_border = {"rmass", "vfrac", "s0", "x0"};
fields_border_vel = {"rmass", "vfrac", "s0", "x0"};
fields_exchange = {"rmass", "vfrac", "s0", "x0"};
fields_restart = {"rmass", "vfrac", "s0", "x0"};
fields_create = {"rmass", "vfrac", "s0", "x0"};
fields_data_atom = {"id", "type", "vfrac", "rmass", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -110,8 +107,7 @@ void AtomVecPeri::data_atom_post(int ilocal)
x0[ilocal][1] = x[ilocal][1];
x0[ilocal][2] = x[ilocal][2];
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid mass in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid mass in Atoms section of data file");
}
/* ----------------------------------------------------------------------
@ -119,10 +115,10 @@ void AtomVecPeri::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecPeri::property_atom(char *name)
int AtomVecPeri::property_atom(const std::string &name)
{
if (strcmp(name,"vfrac") == 0) return 0;
if (strcmp(name,"s0") == 0) return 1;
if (name == "vfrac") return 0;
if (name == "s0") return 1;
return -1;
}
@ -131,8 +127,7 @@ int AtomVecPeri::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecPeri::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecPeri::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -140,14 +135,18 @@ void AtomVecPeri::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = vfrac[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = vfrac[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = s0[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = s0[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/PERI/atom_vec_peri.h
View File

@ -31,7 +31,7 @@ class AtomVecPeri : public AtomVec {
void grow_pointers() override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

2
src/PHONON/dynamical_matrix.cpp
View File

@ -431,7 +431,7 @@ void DynamicalMatrix::update_force()
force_clear();
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
if (n_pre_force) {
modify->pre_force(vflag);

2
src/PHONON/third_order.cpp
View File

@ -487,7 +487,7 @@ void ThirdOrder::update_force()
neighbor->ago = 0;
if (modify->get_fix_by_id("package_intel")) neighbor->decide();
force_clear();
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;

2
src/REPLICA/verlet_split.cpp
View File

@ -300,7 +300,7 @@ void VerletSplit::run(int n)
int n_pre_neighbor = modify->n_pre_neighbor;
int n_pre_force = modify->n_pre_force;
int n_pre_reverse = modify->n_pre_reverse;
int n_post_force = modify->n_post_force;
int n_post_force = modify->n_post_force_any;
int n_end_of_step = modify->n_end_of_step;
if (atom->sortfreq > 0) sortflag = 1;

76
src/SPH/atom_vec_sph.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -16,8 +15,6 @@
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -38,18 +35,18 @@ AtomVecSPH::AtomVecSPH(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rho drho esph desph cv vest";
fields_copy = (char *) "rho drho esph desph cv vest";
fields_comm = (char *) "rho esph vest";
fields_comm_vel = (char *) "rho esph vest";
fields_reverse = (char *) "drho desph";
fields_border = (char *) "rho esph cv vest";
fields_border_vel = (char *) "rho esph cv vest";
fields_exchange = (char *) "rho esph cv vest";
fields_restart = (char * ) "rho esph cv vest";
fields_create = (char *) "rho esph cv vest desph drho";
fields_data_atom = (char *) "id type rho esph cv x";
fields_data_vel = (char *) "id v";
fields_grow = {"rho", "drho", "esph", "desph", "cv", "vest"};
fields_copy = {"rho", "drho", "esph", "desph", "cv", "vest"};
fields_comm = {"rho", "esph", "vest"};
fields_comm_vel = {"rho", "esph", "vest"};
fields_reverse = {"drho", "desph"};
fields_border = {"rho", "esph", "cv", "vest"};
fields_border_vel = {"rho", "esph", "cv", "vest"};
fields_exchange = {"rho", "esph", "cv", "vest"};
fields_restart = {"rho", "esph", "cv", "vest"};
fields_create = {"rho", "esph", "cv", "vest", "desph", "drho"};
fields_data_atom = {"id", "type", "rho", "esph", "cv", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -76,8 +73,8 @@ void AtomVecSPH::grow_pointers()
void AtomVecSPH::force_clear(int n, size_t nbytes)
{
memset(&desph[n],0,nbytes);
memset(&drho[n],0,nbytes);
memset(&desph[n], 0, nbytes);
memset(&drho[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
@ -108,13 +105,13 @@ void AtomVecSPH::data_atom_post(int ilocal)
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecSPH::property_atom(char *name)
int AtomVecSPH::property_atom(const std::string &name)
{
if (strcmp(name,"rho") == 0) return 0;
if (strcmp(name,"drho") == 0) return 1;
if (strcmp(name,"esph") == 0) return 2;
if (strcmp(name,"desph") == 0) return 3;
if (strcmp(name,"cv") == 0) return 4;
if (name == "rho") return 0;
if (name == "drho") return 1;
if (name == "esph") return 2;
if (name == "desph") return 3;
if (name == "cv") return 4;
return -1;
}
@ -123,8 +120,7 @@ int AtomVecSPH::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecSPH::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
void AtomVecSPH::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -132,32 +128,42 @@ void AtomVecSPH::pack_property_atom(int index, double *buf,
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = rho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = rho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = drho[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = drho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = esph[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = esph[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = desph[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = desph[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 4) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = cv[i];
else buf[n] = 0.0;
if (mask[i] & groupbit)
buf[n] = cv[i];
else
buf[n] = 0.0;
n += nvalues;
}
}

2
src/SPH/atom_vec_sph.h
View File

@ -32,7 +32,7 @@ class AtomVecSPH : public AtomVec {
void force_clear(int, size_t) override;
void create_atom_post(int) override;
void data_atom_post(int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:

37
src/SPIN/atom_vec_spin.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
@ -25,10 +24,11 @@
------------------------------------------------------------------------- */
#include "atom_vec_spin.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include <cmath>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -46,18 +46,18 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "sp fm fm_long";
fields_copy = (char *) "sp";
fields_comm = (char *) "sp";
fields_comm_vel = (char *) "sp";
fields_reverse = (char *) "fm fm_long";
fields_border = (char *) "sp";
fields_border_vel = (char *) "sp";
fields_exchange = (char *) "sp";
fields_restart = (char *) "sp";
fields_create = (char *) "sp";
fields_data_atom = (char *) "id type x sp";
fields_data_vel = (char *) "id v";
fields_grow = {"sp", "fm", "fm_long"};
fields_copy = {"sp"};
fields_comm = {"sp"};
fields_comm_vel = {"sp"};
fields_reverse = {"fm", "fm_long"};
fields_border = {"sp"};
fields_border_vel = {"sp"};
fields_exchange = {"sp"};
fields_restart = {"sp"};
fields_create = {"sp"};
fields_data_atom = {"id", "type", "x", "sp"};
fields_data_vel = {"id", "v"};
setup_fields();
}
@ -82,8 +82,8 @@ void AtomVecSpin::grow_pointers()
void AtomVecSpin::force_clear(int n, size_t nbytes)
{
memset(&fm[n][0],0,3*nbytes);
memset(&fm_long[n][0],0,3*nbytes);
memset(&fm[n][0], 0, 3 * nbytes);
memset(&fm_long[n][0], 0, 3 * nbytes);
}
/* ----------------------------------------------------------------------
@ -94,8 +94,7 @@ void AtomVecSpin::force_clear(int n, size_t nbytes)
void AtomVecSpin::data_atom_post(int ilocal)
{
double *sp_one = sp[ilocal];
double norm =
1.0/sqrt(sp_one[0]*sp_one[0] + sp_one[1]*sp_one[1] + sp_one[2]*sp_one[2]);
double norm = 1.0 / sqrt(sp_one[0] * sp_one[0] + sp_one[1] * sp_one[1] + sp_one[2] * sp_one[2]);
sp_one[0] *= norm;
sp_one[1] *= norm;
sp_one[2] *= norm;

12
src/angle.cpp
View File

@ -354,3 +354,15 @@ double Angle::memory_usage()
bytes += (double) comm->nthreads * maxcvatom * 9 * sizeof(double);
return bytes;
}
/* -----------------------------------------------------------------------
reset all type-based angle params via init()
-------------------------------------------------------------------------- */
void Angle::reinit()
{
if (!reinitflag)
error->all(FLERR, "Fix adapt interface to this angle style not supported");
init();
}

5
src/angle.h
View File

@ -37,6 +37,9 @@ class Angle : protected Pointers {
// CENTROID_AVAIL = different and implemented
// CENTROID_NOTAVAIL = different, not yet implemented
int reinitflag; // 0 if not compatible with fix adapt
// extract() method may still need to be added
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
@ -63,6 +66,8 @@ class Angle : protected Pointers {
du2 = 0.0;
}
virtual double memory_usage();
virtual void *extract(const char *, int &) { return nullptr; }
void reinit();
protected:
int suffix_flag; // suffix compatibility flag

76
src/atom.cpp
View File

@ -47,7 +47,6 @@ using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 1
#define DELTA_PERATOM 64
#define EPSILON 1.0e-6
/* ----------------------------------------------------------------------
@ -105,11 +104,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
binhead = nullptr;
next = permute = nullptr;
// data structure with info on per-atom vectors/arrays
nperatom = maxperatom = 0;
peratom = nullptr;
// --------------------------------------------------------------------
// 1st customization section: customize by adding new per-atom variables
@ -286,11 +280,11 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
Atom::~Atom()
{
delete [] atom_style;
delete[] atom_style;
delete avec;
delete avec_map;
delete [] firstgroupname;
delete[] firstgroupname;
memory->destroy(binhead);
memory->destroy(next);
memory->destroy(permute);
@ -303,12 +297,6 @@ Atom::~Atom()
memory->destroy(v);
memory->destroy(f);
// delete peratom data struct
for (int i = 0; i < nperatom; i++)
delete [] peratom[i].name;
memory->sfree(peratom);
// delete custom atom arrays
for (int i = 0; i < nivector; i++) {
@ -385,12 +373,7 @@ void Atom::settings(Atom *old)
void Atom::peratom_create()
{
for (int i = 0; i < nperatom; i++)
delete [] peratom[i].name;
memory->sfree(peratom);
peratom = nullptr;
nperatom = maxperatom = 0;
peratom.clear();
// --------------------------------------------------------------------
// 2nd customization section: add peratom variables here, order does not matter
@ -571,23 +554,11 @@ void Atom::peratom_create()
use add_peratom_vary() when column count varies per atom
------------------------------------------------------------------------- */
void Atom::add_peratom(const char *name, void *address,
void Atom::add_peratom(const std::string &name, void *address,
int datatype, int cols, int threadflag)
{
if (nperatom == maxperatom) {
maxperatom += DELTA_PERATOM;
peratom = (PerAtom *)
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = cols;
peratom[nperatom].threadflag = threadflag;
peratom[nperatom].address_length = nullptr;
nperatom++;
PerAtom item = {name, address, nullptr, nullptr, datatype, cols, 0, threadflag};
peratom.push_back(item);
}
/* ----------------------------------------------------------------------
@ -596,15 +567,13 @@ void Atom::add_peratom(const char *name, void *address,
see atom_style tdpd as an example
------------------------------------------------------------------------- */
void Atom::add_peratom_change_columns(const char *name, int cols)
void Atom::add_peratom_change_columns(const std::string &name, int cols)
{
for (int i = 0; i < nperatom; i++) {
if (strcmp(name,peratom[i].name) == 0) {
peratom[i].cols = cols;
return;
}
}
error->all(FLERR,"Could not find name of peratom array for column change");
auto match = std::find_if(peratom.begin(), peratom.end(),
[&name] (const PerAtom &p) { return p.name == name; });
if (match != peratom.end()) (*match).cols = cols;
else error->all(FLERR,"Could not find per-atom array name {} for column change", name);
}
/* ----------------------------------------------------------------------
@ -619,25 +588,11 @@ void Atom::add_peratom_change_columns(const char *name, int cols)
e.g. nspecial
------------------------------------------------------------------------- */
void Atom::add_peratom_vary(const char *name, void *address,
void Atom::add_peratom_vary(const std::string &name, void *address,
int datatype, int *cols, void *length, int collength)
{
if (nperatom == maxperatom) {
maxperatom += DELTA_PERATOM;
peratom = (PerAtom *)
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = -1;
peratom[nperatom].threadflag = 0;
peratom[nperatom].address_maxcols = cols;
peratom[nperatom].address_length = length;
peratom[nperatom].collength = collength;
nperatom++;
PerAtom item = {name, address, length, cols, datatype, -1, collength, 0};
peratom.push_back(item);
}
/* ----------------------------------------------------------------------
@ -2917,4 +2872,3 @@ double Atom::memory_usage()
return bytes;
}

11
src/atom.h
View File

@ -213,7 +213,7 @@ class Atom : protected Pointers {
// per-atom data struct describing all per-atom vectors/arrays
struct PerAtom {
char *name;
std::string name;
void *address;
void *address_length;
int *address_maxcols;
@ -223,8 +223,7 @@ class Atom : protected Pointers {
int threadflag;
};
PerAtom *peratom;
int nperatom, maxperatom;
std::vector<PerAtom> peratom;
// custom vectors and arrays used by fix property/atom
@ -293,9 +292,9 @@ class Atom : protected Pointers {
void settings(class Atom *);
void peratom_create();
void add_peratom(const char *, void *, int, int, int threadflag = 0);
void add_peratom_change_columns(const char *, int);
void add_peratom_vary(const char *, void *, int, int *, void *, int collength = 0);
void add_peratom(const std::string &, void *, int, int, int threadflag = 0);
void add_peratom_change_columns(const std::string &, int);
void add_peratom_vary(const std::string &, void *, int, int *, void *, int collength = 0);
void create_avec(const std::string &, int, char **, int);
virtual AtomVec *new_avec(const std::string &, int, int &);

967
src/atom_vec.cpp
View File

File diff suppressed because it is too large Load Diff

22
src/atom_vec.h
View File

@ -59,11 +59,10 @@ class AtomVec : protected Pointers {
// additional list of peratom fields operated on by different methods
// set or created by child styles
char *fields_grow, *fields_copy;
char *fields_comm, *fields_comm_vel, *fields_reverse;
char *fields_border, *fields_border_vel;
char *fields_exchange, *fields_restart;
char *fields_create, *fields_data_atom, *fields_data_vel;
std::vector<std::string> fields_grow, fields_copy, fields_comm, fields_comm_vel;
std::vector<std::string> fields_reverse, fields_border, fields_border_vel;
std::vector<std::string> fields_exchange, fields_restart, fields_create;
std::vector<std::string> fields_data_atom, fields_data_vel;
// methods
@ -152,7 +151,7 @@ class AtomVec : protected Pointers {
virtual int pack_data_bonus(double *, int) { return 0; }
virtual void write_data_bonus(FILE *, int, double *, int) {}
virtual int property_atom(char *) { return -1; }
virtual int property_atom(const std::string &) { return -1; }
virtual void pack_property_atom(int, double *, int, int) {}
virtual double memory_usage();
@ -187,11 +186,10 @@ class AtomVec : protected Pointers {
// standard list of peratom fields always operated on by different methods
// common to all styles, so not listed in field strings
const char *default_grow, *default_copy;
const char *default_comm, *default_comm_vel, *default_reverse;
const char *default_border, *default_border_vel;
const char *default_exchange, *default_restart;
const char *default_create, *default_data_atom, *default_data_vel;
static const std::vector<std::string> default_grow, default_copy, default_comm, default_comm_vel;
static const std::vector<std::string> default_reverse, default_border, default_border_vel;
static const std::vector<std::string> default_exchange, default_restart, default_create;
static const std::vector<std::string> default_data_atom, default_data_vel;
struct Method {
std::vector<void *> pdata;
@ -223,7 +221,7 @@ class AtomVec : protected Pointers {
void grow_nmax();
int grow_nmax_bonus(int);
void setup_fields();
int process_fields(char *, const char *, Method *);
int process_fields(const std::vector<std::string> &, const std::vector<std::string> &, Method *);
void init_method(int, Method *);
};

15
src/atom_vec_atomic.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -30,18 +29,8 @@ AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "";
fields_copy = (char *) "";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "";
fields_border_vel = (char *) "";
fields_exchange = (char *) "";
fields_restart = (char *) "";
fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

223
src/atom_vec_body.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,8 +22,6 @@
#include "modify.h"
#include "my_pool_chunk.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -54,27 +51,29 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
bptr = nullptr;
if (sizeof(double) == sizeof(int)) intdoubleratio = 1;
else if (sizeof(double) == 2*sizeof(int)) intdoubleratio = 2;
else error->all(FLERR,"Internal error in atom_style body");
if (sizeof(double) == sizeof(int))
intdoubleratio = 1;
else if (sizeof(double) == 2 * sizeof(int))
intdoubleratio = 2;
else
error->all(FLERR, "Internal error in atom_style body");
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "radius rmass angmom torque body";
fields_copy = (char *) "radius rmass angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "radius rmass";
fields_border_vel = (char *) "radius rmass angmom";
fields_exchange = (char *) "radius rmass angmom";
fields_restart = (char *) "radius rmass angmom";
fields_create = (char *) "radius rmass angmom body";
fields_data_atom = (char *) "id type body rmass x";
fields_data_vel = (char *) "id v angmom";
fields_grow = {"radius", "rmass", "angmom", "torque", "body"};
fields_copy = {"radius", "rmass", "angmom"};
fields_comm_vel = {"angmom"};
fields_reverse = {"torque"};
fields_border = {"radius", "rmass"};
fields_border_vel = {"radius", "rmass", "angmom"};
fields_exchange = {"radius", "rmass", "angmom"};
fields_restart = {"radius", "rmass", "angmom"};
fields_create = {"radius", "rmass", "angmom", "body"};
fields_data_atom = {"id", "type", "body", "rmass", "x"};
fields_data_vel = {"id", "v", "angmom"};
}
/* ---------------------------------------------------------------------- */
@ -101,23 +100,25 @@ void AtomVecBody::process_args(int narg, char **arg)
{
// suppress unused parameter warning dependent on style_body.h
(void)(arg);
(void) (arg);
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
if (narg < 1) error->all(FLERR, "Invalid atom_style body command");
if (false) { // NOLINT
if (false) { // NOLINT
bptr = nullptr;
#define BODY_CLASS
#define BodyStyle(key,Class) \
} else if (strcmp(arg[0],#key) == 0) { \
bptr = new Class(lmp,narg,arg);
#include "style_body.h" // IWYU pragma: keep
#define BodyStyle(key, Class) \
} \
else if (strcmp(arg[0], #key) == 0) \
{ \
bptr = new Class(lmp, narg, arg);
#include "style_body.h" // IWYU pragma: keep
#undef BodyStyle
#undef BODY_CLASS
} else error->all(FLERR,utils::
check_packages_for_style("body",arg[0],lmp).c_str());
} else
error->all(FLERR, utils::check_packages_for_style("body", arg[0], lmp).c_str());
bptr->avec = this;
icp = bptr->icp;
@ -153,11 +154,9 @@ void AtomVecBody::grow_pointers()
void AtomVecBody::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -173,7 +172,7 @@ void AtomVecBody::copy_bonus(int i, int j, int delflag)
int k = body[j];
icp->put(bonus[k].iindex);
dcp->put(bonus[k].dindex);
copy_bonus_all(nlocal_bonus-1,k);
copy_bonus_all(nlocal_bonus - 1, k);
nlocal_bonus--;
}
@ -192,7 +191,7 @@ void AtomVecBody::copy_bonus(int i, int j, int delflag)
void AtomVecBody::copy_bonus_all(int i, int j)
{
body[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -218,7 +217,7 @@ void AtomVecBody::clear_bonus()
int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -230,7 +229,7 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
buf[m++] = quat[1];
buf[m++] = quat[2];
buf[m++] = quat[3];
m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
m += bptr->pack_comm_body(&bonus[body[j]], &buf[m]);
}
}
@ -241,7 +240,7 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -253,7 +252,7 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
quat[1] = buf[m++];
quat[2] = buf[m++];
quat[3] = buf[m++];
m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
m += bptr->unpack_comm_body(&bonus[body[i]], &buf[m]);
}
}
}
@ -262,13 +261,14 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*inertia;
int i, j, m;
double *quat, *inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (body[j] < 0) buf[m++] = ubuf(0).d;
if (body[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[body[j]].quat;
@ -282,7 +282,7 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
m += bptr->pack_border_body(&bonus[body[j]], &buf[m]);
}
}
@ -293,14 +293,15 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*inertia;
int i, j, m, last;
double *quat, *inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
body[i] = (int) ubuf(buf[m++]).i;
if (body[i] == 0) body[i] = -1;
if (body[i] == 0)
body[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -316,9 +317,9 @@ int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in clear_bonus()
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
bonus[j].ivalue = icp->get(bonus[j].ninteger, bonus[j].iindex);
bonus[j].dvalue = dcp->get(bonus[j].ndouble, bonus[j].dindex);
m += bptr->unpack_border_body(&bonus[j], &buf[m]);
bonus[j].ilocal = i;
body[i] = j;
nghost_bonus++;
@ -337,7 +338,8 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (body[i] < 0) buf[m++] = ubuf(0).d;
if (body[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
@ -352,10 +354,12 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
memcpy(&buf[m], bonus[j].ivalue, bonus[j].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[j].ninteger;
else
m += (bonus[j].ninteger + 1) / 2;
memcpy(&buf[m], bonus[j].dvalue, bonus[j].ndouble * sizeof(double));
m += bonus[j].ndouble;
}
@ -369,7 +373,8 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
if (body[ilocal] == 0)
body[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -384,16 +389,14 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
// corresponding put() calls are in copy()
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger, bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble, bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue, &buf[m], bonus[nlocal_bonus].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[nlocal_bonus].ninteger;
else
m += (bonus[nlocal_bonus].ninteger + 1) / 2;
memcpy(bonus[nlocal_bonus].dvalue, &buf[m], bonus[nlocal_bonus].ndouble * sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = ilocal;
@ -416,10 +419,13 @@ int AtomVecBody::size_restart_bonus()
for (i = 0; i < nlocal; i++) {
if (body[i] >= 0) {
n += size_restart_bonus_one;
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
else n += (bonus[body[i]].ninteger+1)/2;
if (intdoubleratio == 1)
n += bonus[body[i]].ninteger;
else
n += (bonus[body[i]].ninteger + 1) / 2;
n += bonus[body[i]].ndouble;
} else n++;
} else
n++;
}
return n;
@ -435,7 +441,8 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (body[i] < 0) buf[m++] = ubuf(0).d;
if (body[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = body[i];
@ -450,10 +457,12 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
buf[m++] = inertia[2];
buf[m++] = ubuf(bonus[j].ninteger).d;
buf[m++] = ubuf(bonus[j].ndouble).d;
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[j].ninteger;
else m += (bonus[j].ninteger+1)/2;
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
memcpy(&buf[m], bonus[j].ivalue, bonus[j].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[j].ninteger;
else
m += (bonus[j].ninteger + 1) / 2;
memcpy(&buf[m], bonus[j].dvalue, bonus[j].ndouble * sizeof(double));
m += bonus[j].ndouble;
}
@ -469,7 +478,8 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
if (body[ilocal] == 0)
body[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -483,16 +493,14 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
inertia[2] = buf[m++];
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
bonus[nlocal_bonus].ninteger*sizeof(int));
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
else m += (bonus[nlocal_bonus].ninteger+1)/2;
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
bonus[nlocal_bonus].ndouble*sizeof(double));
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger, bonus[nlocal_bonus].iindex);
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble, bonus[nlocal_bonus].dindex);
memcpy(bonus[nlocal_bonus].ivalue, &buf[m], bonus[nlocal_bonus].ninteger * sizeof(int));
if (intdoubleratio == 1)
m += bonus[nlocal_bonus].ninteger;
else
m += (bonus[nlocal_bonus].ninteger + 1) / 2;
memcpy(bonus[nlocal_bonus].dvalue, &buf[m], bonus[nlocal_bonus].ndouble * sizeof(double));
m += bonus[nlocal_bonus].ndouble;
bonus[nlocal_bonus].ilocal = ilocal;
body[ilocal] = nlocal_bonus++;
@ -521,13 +529,15 @@ void AtomVecBody::create_atom_post(int ilocal)
void AtomVecBody::data_atom_post(int ilocal)
{
body_flag = body[ilocal];
if (body_flag == 0) body_flag = -1;
else if (body_flag == 1) body_flag = 0;
else error->one(FLERR,"Invalid body flag in Atoms section of data file");
if (body_flag == 0)
body_flag = -1;
else if (body_flag == 1)
body_flag = 0;
else
error->one(FLERR, "Invalid body flag in Atoms section of data file");
body[ilocal] = body_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
radius[ilocal] = 0.5;
angmom[ilocal][0] = 0.0;
@ -539,14 +549,12 @@ void AtomVecBody::data_atom_post(int ilocal)
unpack one body from Bodies section of data file
------------------------------------------------------------------------- */
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
int *ivalues, double *dvalues)
void AtomVecBody::data_body(int m, int ninteger, int ndouble, int *ivalues, double *dvalues)
{
if (body[m])
error->one(FLERR,"Assigning body parameters to non-body atom");
if (body[m]) error->one(FLERR, "Assigning body parameters to non-body atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].ilocal = m;
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
bptr->data_body(nlocal_bonus, ninteger, ndouble, ivalues, dvalues);
body[m] = nlocal_bonus++;
}
@ -557,14 +565,14 @@ void AtomVecBody::data_body(int m, int ninteger, int ndouble,
double AtomVecBody::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
bytes += icp->size() + dcp->size();
int nall = nlocal_bonus + nghost_bonus;
for (int i = 0; i < nall; i++) {
if (body[i] >= 0) {
bytes += (double)bonus[body[i]].ninteger * sizeof(int);
bytes += (double)bonus[body[i]].ndouble * sizeof(double);
bytes += (double) bonus[body[i]].ninteger * sizeof(int);
bytes += (double) bonus[body[i]].ndouble * sizeof(double);
}
}
@ -579,8 +587,10 @@ void AtomVecBody::pack_data_pre(int ilocal)
{
body_flag = body[ilocal];
if (body_flag < 0) body[ilocal] = 0;
else body[ilocal] = 1;
if (body_flag < 0)
body[ilocal] = 0;
else
body[ilocal] = 1;
}
/* ----------------------------------------------------------------------
@ -598,7 +608,7 @@ int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
int m = 0;
for (i = 0; i < nlocal; i++) {
if (body[i] < 0) continue;
int n = bptr->pack_data_body(tag[i],body[i],buf);
int n = bptr->pack_data_body(tag[i], body[i], buf);
m += n;
if (buf) buf += n;
}
@ -613,9 +623,7 @@ int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
i += bptr->write_data_body(fp,&buf[i]);
}
while (i < n) { i += bptr->write_data_body(fp, &buf[i]); }
}
/* ----------------------------------------------------------------------
@ -631,10 +639,9 @@ void AtomVecBody::pack_data_post(int ilocal)
body computes its size based on ivalues/dvalues and returns it
------------------------------------------------------------------------- */
double AtomVecBody::radius_body(int ninteger, int ndouble,
int *ivalues, double *dvalues)
double AtomVecBody::radius_body(int ninteger, int ndouble, int *ivalues, double *dvalues)
{
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
return bptr->radius_body(ninteger, ndouble, ivalues, dvalues);
}
/* ----------------------------------------------------------------------
@ -644,10 +651,12 @@ double AtomVecBody::radius_body(int ninteger, int ndouble,
void AtomVecBody::set_quat(int m, double *quat_external)
{
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
if (body[m] < 0) error->one(FLERR, "Assigning quat to non-body atom");
double *quat = bonus[body[m]].quat;
quat[0] = quat_external[0]; quat[1] = quat_external[1];
quat[2] = quat_external[2]; quat[3] = quat_external[3];
quat[0] = quat_external[0];
quat[1] = quat_external[1];
quat[2] = quat_external[2];
quat[3] = quat_external[3];
}
/* ----------------------------------------------------------------------

22
src/atom_vec_charge.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -31,18 +30,15 @@ AtomVecCharge::AtomVecCharge(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "q";
fields_copy = (char *) "q";
fields_comm = (char *) "";
fields_comm_vel = (char *) "";
fields_reverse = (char *) "";
fields_border = (char *) "q";
fields_border_vel = (char *) "q";
fields_exchange = (char *) "q";
fields_restart = (char *) "q";
fields_create = (char *) "q";
fields_data_atom = (char *) "id type q x";
fields_data_vel = (char *) "id v";
fields_grow = {"q"};
fields_copy = {"q"};
fields_border = {"q"};
fields_border_vel = {"q"};
fields_exchange = {"q"};
fields_restart = {"q"};
fields_create = {"q"};
fields_data_atom = {"id", "type", "q", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}

136
src/atom_vec_ellipsoid.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -26,10 +25,8 @@
#include "memory.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
/* ---------------------------------------------------------------------- */
@ -54,18 +51,17 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "rmass angmom torque ellipsoid";
fields_copy = (char *) "rmass angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "rmass";
fields_border_vel = (char *) "rmass angmom";
fields_exchange = (char *) "rmass angmom";
fields_restart = (char *) "rmass angmom";
fields_create = (char *) "rmass angmom ellipsoid";
fields_data_atom = (char *) "id type ellipsoid rmass x";
fields_data_vel = (char *) "id v angmom";
fields_grow = {"rmass", "angmom", "torque", "ellipsoid"};
fields_copy = {"rmass", "angmom"};
fields_comm_vel = {"angmom"};
fields_reverse = {"torque"};
fields_border = {"rmass"};
fields_border_vel = {"rmass", "angmom"};
fields_exchange = {"rmass", "angmom"};
fields_restart = {"rmass", "angmom"};
fields_create = {"rmass", "angmom", "ellipsoid"};
fields_data_atom = {"id", "type", "ellipsoid", "rmass", "x"};
fields_data_vel = {"id", "v", "angmom"};
setup_fields();
}
@ -96,11 +92,9 @@ void AtomVecEllipsoid::grow_pointers()
void AtomVecEllipsoid::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -112,7 +106,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && ellipsoid[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[j]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[j]);
nlocal_bonus--;
}
@ -131,7 +125,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
void AtomVecEllipsoid::copy_bonus_all(int i, int j)
{
ellipsoid[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -152,7 +146,7 @@ void AtomVecEllipsoid::clear_bonus()
int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -174,7 +168,7 @@ int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -194,13 +188,14 @@ void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *shape,*quat;
int i, j, m;
double *shape, *quat;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
shape = bonus[ellipsoid[j]].shape;
@ -222,14 +217,15 @@ int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
int AtomVecEllipsoid::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *shape,*quat;
int i, j, m, last;
double *shape, *quat;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
ellipsoid[i] = (int) ubuf(buf[m++]).i;
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
if (ellipsoid[i] == 0)
ellipsoid[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -260,7 +256,8 @@ int AtomVecEllipsoid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -285,7 +282,8 @@ int AtomVecEllipsoid::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -316,8 +314,10 @@ int AtomVecEllipsoid::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (ellipsoid[i] >= 0) n += size_restart_bonus_one;
else n++;
if (ellipsoid[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -333,7 +333,8 @@ int AtomVecEllipsoid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
if (ellipsoid[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = ellipsoid[i];
@ -358,7 +359,8 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
if (ellipsoid[ilocal] == 0)
ellipsoid[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
@ -381,32 +383,31 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
unpack one line from Ellipsoids section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & values)
void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (ellipsoid[m])
error->one(FLERR,"Assigning ellipsoid parameters to non-ellipsoid atom");
if (ellipsoid[m]) error->one(FLERR, "Assigning ellipsoid parameters to non-ellipsoid atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *shape = bonus[nlocal_bonus].shape;
int ivalue = 1;
shape[0] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[1] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[2] = 0.5 * utils::numeric(FLERR,values[ivalue++],true,lmp);
shape[0] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[1] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
shape[2] = 0.5 * utils::numeric(FLERR, values[ivalue++], true, lmp);
if (shape[0] <= 0.0 || shape[1] <= 0.0 || shape[2] <= 0.0)
error->one(FLERR,"Invalid shape in Ellipsoids section of data file");
error->one(FLERR, "Invalid shape in Ellipsoids section of data file");
double *quat = bonus[nlocal_bonus].quat;
quat[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[3] = utils::numeric(FLERR,values[ivalue++],true,lmp);
quat[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
quat[3] = utils::numeric(FLERR, values[ivalue++], true, lmp);
MathExtra::qnormalize(quat);
// reset ellipsoid mass
// previously stored density in rmass
rmass[m] *= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[m] *= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
bonus[nlocal_bonus].ilocal = m;
ellipsoid[m] = nlocal_bonus++;
@ -419,7 +420,7 @@ void AtomVecEllipsoid::data_atom_bonus(int m, const std::vector<std::string> & v
double AtomVecEllipsoid::memory_usage_bonus()
{
double bytes = 0;
bytes += nmax_bonus*sizeof(Bonus);
bytes += nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -441,13 +442,15 @@ void AtomVecEllipsoid::create_atom_post(int ilocal)
void AtomVecEllipsoid::data_atom_post(int ilocal)
{
ellipsoid_flag = ellipsoid[ilocal];
if (ellipsoid_flag == 0) ellipsoid_flag = -1;
else if (ellipsoid_flag == 1) ellipsoid_flag = 0;
else error->one(FLERR,"Invalid ellipsoid flag in Atoms section of data file");
if (ellipsoid_flag == 0)
ellipsoid_flag = -1;
else if (ellipsoid_flag == 1)
ellipsoid_flag = 0;
else
error->one(FLERR, "Invalid ellipsoid flag in Atoms section of data file");
ellipsoid[ilocal] = ellipsoid_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
angmom[ilocal][0] = 0.0;
angmom[ilocal][1] = 0.0;
@ -465,12 +468,14 @@ void AtomVecEllipsoid::pack_data_pre(int ilocal)
ellipsoid_flag = atom->ellipsoid[ilocal];
rmass_one = atom->rmass[ilocal];
if (ellipsoid_flag < 0) ellipsoid[ilocal] = 0;
else ellipsoid[ilocal] = 1;
if (ellipsoid_flag < 0)
ellipsoid[ilocal] = 0;
else
ellipsoid[ilocal] = 1;
if (ellipsoid_flag >= 0) {
shape = bonus[ellipsoid_flag].shape;
rmass[ilocal] /= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * shape[0] * shape[1] * shape[2];
}
}
@ -491,7 +496,7 @@ void AtomVecEllipsoid::pack_data_post(int ilocal)
int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
int i, j;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
@ -502,14 +507,15 @@ int AtomVecEllipsoid::pack_data_bonus(double *buf, int /*flag*/)
if (buf) {
buf[m++] = ubuf(tag[i]).d;
j = ellipsoid[i];
buf[m++] = 2.0*bonus[j].shape[0];
buf[m++] = 2.0*bonus[j].shape[1];
buf[m++] = 2.0*bonus[j].shape[2];
buf[m++] = 2.0 * bonus[j].shape[0];
buf[m++] = 2.0 * bonus[j].shape[1];
buf[m++] = 2.0 * bonus[j].shape[2];
buf[m++] = bonus[j].quat[0];
buf[m++] = bonus[j].quat[1];
buf[m++] = bonus[j].quat[2];
buf[m++] = bonus[j].quat[3];
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
@ -523,8 +529,8 @@ void AtomVecEllipsoid::write_data_bonus(FILE *fp, int n, double *buf, int /*flag
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {} {} {} {}\n",ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4],buf[i+5],buf[i+6],buf[i+7]);
fmt::print(fp, "{} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7]);
i += size_data_bonus;
}
}
@ -552,7 +558,7 @@ void AtomVecEllipsoid::set_shape(int i, double shapex, double shapey, double sha
bonus[nlocal_bonus].ilocal = i;
ellipsoid[i] = nlocal_bonus++;
} else if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) {
copy_bonus_all(nlocal_bonus-1,ellipsoid[i]);
copy_bonus_all(nlocal_bonus - 1, ellipsoid[i]);
nlocal_bonus--;
ellipsoid[i] = -1;
} else {

322
src/atom_vec_hybrid.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,12 +18,12 @@
#include "error.h"
#include "tokenizer.h"
#include <algorithm>
#include <cstring>
using namespace LAMMPS_NS;
#define NFIELDSTRINGS 12 // # of field strings
enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in WriteData
enum { ELLIPSOID, LINE, TRIANGLE, BODY }; // also in WriteData
/* ---------------------------------------------------------------------- */
@ -33,22 +32,16 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
nstyles = 0;
styles = nullptr;
keywords = nullptr;
fieldstrings = nullptr;
bonus_flag = 0;
nstyles_bonus = 0;
styles_bonus = nullptr;
// these strings will be concatenated from sub-style strings
// field strings will be concatenated from sub-style strings
// fields_data_atom & fields_data_vel start with fields common to all styles
fields_grow = fields_copy = fields_comm = fields_comm_vel = (char *) "";
fields_reverse = fields_border = fields_border_vel = (char *) "";
fields_exchange = fields_restart = fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_allocated = 0;
fields_data_atom = {"id", "type", "x"};
fields_data_vel = {"id", "v"};
}
/* ---------------------------------------------------------------------- */
@ -56,28 +49,10 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
AtomVecHybrid::~AtomVecHybrid()
{
for (int k = 0; k < nstyles; k++) delete styles[k];
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
delete [] styles_bonus;
if (!fields_allocated) return;
delete [] fields_grow;
delete [] fields_copy;
delete [] fields_comm;
delete [] fields_comm_vel;
delete [] fields_reverse;
delete [] fields_border;
delete [] fields_border_vel;
delete [] fields_exchange;
delete [] fields_restart;
delete [] fields_create;
delete [] fields_data_atom;
delete [] fields_data_vel;
for (int k = 0; k < nstyles; k++) delete [] fieldstrings[k].fstr;
delete [] fieldstrings;
delete[] styles;
for (int k = 0; k < nstyles; k++) delete[] keywords[k];
delete[] keywords;
delete[] styles_bonus;
}
/* ----------------------------------------------------------------------
@ -92,28 +67,27 @@ void AtomVecHybrid::process_args(int narg, char **arg)
// allocate list of sub-styles as big as possibly needed if no extra args
styles = new AtomVec*[narg];
keywords = new char*[narg];
styles = new AtomVec *[narg];
keywords = new char *[narg];
// allocate each sub-style
// call process_args() with set of args that are not atom style names
// use known_style() to determine which args these are
int i,k,jarg,dummy;
int dummy;
int iarg = 0;
nstyles = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
for (i = 0; i < nstyles; i++)
if (strcmp(arg[iarg],keywords[i]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg],1,dummy);
if (strcmp(arg[iarg], "hybrid") == 0)
error->all(FLERR, "Atom style hybrid cannot have hybrid as an argument");
for (int i = 0; i < nstyles; i++)
if (strcmp(arg[iarg], keywords[i]) == 0)
error->all(FLERR, "Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg], 1, dummy);
keywords[nstyles] = utils::strdup(arg[iarg]);
jarg = iarg + 1;
int jarg = iarg + 1;
while (jarg < narg && !known_style(arg[jarg])) jarg++;
styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]);
styles[nstyles]->process_args(jarg - iarg - 1, &arg[iarg + 1]);
iarg = jarg;
nstyles++;
}
@ -124,20 +98,19 @@ void AtomVecHybrid::process_args(int narg, char **arg)
molecular = Atom::ATOMIC;
maxexchange = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if ((styles[k]->molecular == Atom::MOLECULAR && molecular == Atom::TEMPLATE) ||
(styles[k]->molecular == Atom::TEMPLATE && molecular == Atom::MOLECULAR))
error->all(FLERR,
"Cannot mix molecular and molecule template atom styles");
molecular = MAX(molecular,styles[k]->molecular);
error->all(FLERR, "Cannot mix molecular and molecule template atom styles");
molecular = MAX(molecular, styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow);
mass_type = MAX(mass_type,styles[k]->mass_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
forceclearflag = MAX(forceclearflag,styles[k]->forceclearflag);
bonds_allow = MAX(bonds_allow, styles[k]->bonds_allow);
angles_allow = MAX(angles_allow, styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow, styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow, styles[k]->impropers_allow);
mass_type = MAX(mass_type, styles[k]->mass_type);
dipole_type = MAX(dipole_type, styles[k]->dipole_type);
forceclearflag = MAX(forceclearflag, styles[k]->forceclearflag);
maxexchange += styles[k]->maxexchange;
if (styles[k]->molecular == Atom::TEMPLATE) onemols = styles[k]->onemols;
@ -148,95 +121,71 @@ void AtomVecHybrid::process_args(int narg, char **arg)
int mass_pertype = 0;
int mass_peratom = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if (styles[k]->mass_type == 0) mass_peratom = 1;
if (styles[k]->mass_type == 1) mass_pertype = 1;
}
if (mass_pertype && mass_peratom && comm->me == 0)
error->warning(FLERR, "Atom style hybrid defines both, per-type "
error->warning(FLERR,
"Atom style hybrid defines both, per-type "
"and per-atom masses; both must be set, but only "
"per-atom masses will be used");
// free allstyles created by build_styles()
for (i = 0; i < nallstyles; i++) delete [] allstyles[i];
delete [] allstyles;
// set field strings from all substyles
fieldstrings = new FieldStrings[nstyles];
for (k = 0; k < nstyles; k++) {
fieldstrings[k].fstr = new char*[NFIELDSTRINGS];
fieldstrings[k].fstr[0] = styles[k]->fields_grow;
fieldstrings[k].fstr[1] = styles[k]->fields_copy;
fieldstrings[k].fstr[2] = styles[k]->fields_comm;
fieldstrings[k].fstr[3] = styles[k]->fields_comm_vel;
fieldstrings[k].fstr[4] = styles[k]->fields_reverse;
fieldstrings[k].fstr[5] = styles[k]->fields_border;
fieldstrings[k].fstr[6] = styles[k]->fields_border_vel;
fieldstrings[k].fstr[7] = styles[k]->fields_exchange;
fieldstrings[k].fstr[8] = styles[k]->fields_restart;
fieldstrings[k].fstr[9] = styles[k]->fields_create;
fieldstrings[k].fstr[10] = styles[k]->fields_data_atom;
fieldstrings[k].fstr[11] = styles[k]->fields_data_vel;
}
for (int i = 0; i < nallstyles; i++) delete[] allstyles[i];
delete[] allstyles;
// merge field strings from all sub-styles
// save concat_grow to check for duplicates of special-case fields
char *concat_grow;;
char *dummyptr = nullptr;
std::vector<std::string> concat_grow;
std::vector<std::string> concat_dummy;
fields_grow = merge_fields(0,fields_grow,1,concat_grow);
fields_copy = merge_fields(1,fields_copy,0,dummyptr);
fields_comm = merge_fields(2,fields_comm,0,dummyptr);
fields_comm_vel = merge_fields(3,fields_comm_vel,0,dummyptr);
fields_reverse = merge_fields(4,fields_reverse,0,dummyptr);
fields_border = merge_fields(5,fields_border,0,dummyptr);
fields_border_vel = merge_fields(6,fields_border_vel,0,dummyptr);
fields_exchange = merge_fields(7,fields_exchange,0,dummyptr);
fields_restart = merge_fields(8,fields_restart,0,dummyptr);
fields_create = merge_fields(9,fields_create,0,dummyptr);
fields_data_atom = merge_fields(10,fields_data_atom,0,dummyptr);
fields_data_vel = merge_fields(11,fields_data_vel,0,dummyptr);
fields_allocated = 1;
for (int k = 0; k < nstyles; k++) {
merge_fields(fields_grow, styles[k]->fields_grow, 1, concat_grow);
merge_fields(fields_copy, styles[k]->fields_copy, 0, concat_dummy);
merge_fields(fields_comm, styles[k]->fields_comm, 0, concat_dummy);
merge_fields(fields_comm_vel, styles[k]->fields_comm_vel, 0, concat_dummy);
merge_fields(fields_reverse, styles[k]->fields_reverse, 0, concat_dummy);
merge_fields(fields_border, styles[k]->fields_border, 0, concat_dummy);
merge_fields(fields_border_vel, styles[k]->fields_border_vel, 0, concat_dummy);
merge_fields(fields_exchange, styles[k]->fields_exchange, 0, concat_dummy);
merge_fields(fields_restart, styles[k]->fields_restart, 0, concat_dummy);
merge_fields(fields_create, styles[k]->fields_create, 0, concat_dummy);
merge_fields(fields_data_atom, styles[k]->fields_data_atom, 0, concat_dummy);
merge_fields(fields_data_vel, styles[k]->fields_data_vel, 0, concat_dummy);
}
// check concat_grow for multiple special-case fields
// may cause issues with style-specific create_atom() and data_atom() methods
// issue warnings if appear in multiple sub-styles
const char *dupfield[] = {"radius","rmass"};
int ndupfield = 2;
char *ptr;
std::vector<std::string> dupfield = {"radius", "rmass"};
for (int idup = 0; idup < ndupfield; idup++) {
auto dup = (char *) dupfield[idup];
ptr = strstr(concat_grow,dup);
if ((ptr && strstr(ptr+1,dup)) && (comm->me == 0))
error->warning(FLERR,fmt::format("Per-atom {} is used in multiple sub-"
"styles; must be used consistently",dup));
for (const auto &idup : dupfield) {
if ((comm->me == 0) && (std::count(concat_grow.begin(), concat_grow.end(), idup) > 1))
error->warning(FLERR,
"Per-atom field {} is used in multiple sub-styles; must be used consistently",
idup);
}
delete [] concat_grow;
// set bonus_flag if any substyle has bonus data
// set nstyles_bonus & styles_bonus
// sum two sizes over contributions from each substyle with bonus data.
nstyles_bonus = 0;
for (k = 0; k < nstyles; k++)
for (int k = 0; k < nstyles; k++)
if (styles[k]->bonus_flag) nstyles_bonus++;
if (nstyles_bonus) {
bonus_flag = 1;
styles_bonus = new AtomVec*[nstyles_bonus];
styles_bonus = new AtomVec *[nstyles_bonus];
nstyles_bonus = 0;
size_forward_bonus = 0;
size_border_bonus = 0;
for (k = 0; k < nstyles; k++) {
for (int k = 0; k < nstyles; k++) {
if (styles[k]->bonus_flag) {
styles_bonus[nstyles_bonus++] = styles[k];
size_forward_bonus += styles[k]->size_forward_bonus;
@ -270,23 +219,21 @@ void AtomVecHybrid::grow_pointers()
void AtomVecHybrid::force_clear(int n, size_t nbytes)
{
for (int k = 0; k < nstyles; k++)
if (styles[k]->forceclearflag) styles[k]->force_clear(n,nbytes);
if (styles[k]->forceclearflag) styles[k]->force_clear(n, nbytes);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::copy_bonus(int i, int j, int delflag)
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->copy_bonus(i,j,delflag);
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->copy_bonus(i, j, delflag);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::clear_bonus()
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->clear_bonus();
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->clear_bonus();
}
/* ---------------------------------------------------------------------- */
@ -294,8 +241,7 @@ void AtomVecHybrid::clear_bonus()
int AtomVecHybrid::pack_comm_bonus(int n, int *list, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_comm_bonus(n,list,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_comm_bonus(n, list, buf);
return m;
}
@ -303,8 +249,7 @@ int AtomVecHybrid::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecHybrid::unpack_comm_bonus(int n, int first, double *buf)
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->unpack_comm_bonus(n,first,buf);
for (int k = 0; k < nstyles_bonus; k++) styles_bonus[k]->unpack_comm_bonus(n, first, buf);
}
/* ---------------------------------------------------------------------- */
@ -312,8 +257,7 @@ void AtomVecHybrid::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecHybrid::pack_border_bonus(int n, int *list, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_border_bonus(n,list,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_border_bonus(n, list, buf);
return m;
}
@ -322,8 +266,7 @@ int AtomVecHybrid::pack_border_bonus(int n, int *list, double *buf)
int AtomVecHybrid::unpack_border_bonus(int n, int first, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_border_bonus(n,first,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_border_bonus(n, first, buf);
return m;
}
@ -332,8 +275,7 @@ int AtomVecHybrid::unpack_border_bonus(int n, int first, double *buf)
int AtomVecHybrid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_exchange_bonus(i,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_exchange_bonus(i, buf);
return m;
}
@ -342,8 +284,7 @@ int AtomVecHybrid::pack_exchange_bonus(int i, double *buf)
int AtomVecHybrid::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_exchange_bonus(ilocal,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_exchange_bonus(ilocal, buf);
return m;
}
@ -352,8 +293,7 @@ int AtomVecHybrid::unpack_exchange_bonus(int ilocal, double *buf)
int AtomVecHybrid::size_restart_bonus()
{
int n = 0;
for (int k = 0; k < nstyles_bonus; k++)
n += styles_bonus[k]->size_restart_bonus();
for (int k = 0; k < nstyles_bonus; k++) n += styles_bonus[k]->size_restart_bonus();
return n;
}
@ -362,8 +302,7 @@ int AtomVecHybrid::size_restart_bonus()
int AtomVecHybrid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->pack_restart_bonus(i,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->pack_restart_bonus(i, buf);
return m;
}
@ -372,8 +311,7 @@ int AtomVecHybrid::pack_restart_bonus(int i, double *buf)
int AtomVecHybrid::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
for (int k = 0; k < nstyles_bonus; k++)
m += styles_bonus[k]->unpack_restart_bonus(ilocal,buf);
for (int k = 0; k < nstyles_bonus; k++) m += styles_bonus[k]->unpack_restart_bonus(ilocal, buf);
return m;
}
@ -382,8 +320,7 @@ int AtomVecHybrid::unpack_restart_bonus(int ilocal, double *buf)
double AtomVecHybrid::memory_usage_bonus()
{
double bytes = 0;
for (int k = 0; k < nstyles_bonus; k++)
bytes += styles_bonus[k]->memory_usage_bonus();
for (int k = 0; k < nstyles_bonus; k++) bytes += styles_bonus[k]->memory_usage_bonus();
return bytes;
}
@ -393,8 +330,7 @@ double AtomVecHybrid::memory_usage_bonus()
void AtomVecHybrid::pack_restart_pre(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_restart_pre(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_restart_pre(ilocal);
}
/* ----------------------------------------------------------------------
@ -403,8 +339,7 @@ void AtomVecHybrid::pack_restart_pre(int ilocal)
void AtomVecHybrid::pack_restart_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_restart_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_restart_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -413,8 +348,7 @@ void AtomVecHybrid::pack_restart_post(int ilocal)
void AtomVecHybrid::unpack_restart_init(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->unpack_restart_init(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->unpack_restart_init(ilocal);
}
/* ----------------------------------------------------------------------
@ -423,8 +357,7 @@ void AtomVecHybrid::unpack_restart_init(int ilocal)
void AtomVecHybrid::create_atom_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->create_atom_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->create_atom_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -434,16 +367,15 @@ void AtomVecHybrid::create_atom_post(int ilocal)
void AtomVecHybrid::data_atom_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->data_atom_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->data_atom_post(ilocal);
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_bonds() just unpacked
or initialize other bond quantities
------------------------------------------------------------------------- */
void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1,
tagint atom2, tagint id_offset)
void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1, tagint atom2,
tagint id_offset)
{
for (int k = 0; k < nstyles; k++)
styles[k]->data_bonds_post(m, num_bond, atom1, atom2, id_offset);
@ -455,8 +387,7 @@ void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1,
void AtomVecHybrid::pack_data_pre(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_data_pre(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_data_pre(ilocal);
}
/* ----------------------------------------------------------------------
@ -465,8 +396,7 @@ void AtomVecHybrid::pack_data_pre(int ilocal)
void AtomVecHybrid::pack_data_post(int ilocal)
{
for (int k = 0; k < nstyles; k++)
styles[k]->pack_data_post(ilocal);
for (int k = 0; k < nstyles; k++) styles[k]->pack_data_post(ilocal);
}
/* ----------------------------------------------------------------------
@ -476,12 +406,12 @@ void AtomVecHybrid::pack_data_post(int ilocal)
int AtomVecHybrid::pack_data_bonus(double *buf, int flag)
{
for (int k = 0; k < nstyles; k++) {
if (flag == ELLIPSOID && strcmp(keywords[k],"ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k],"line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k],"tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k],"body") != 0) continue;
if (flag == ELLIPSOID && strcmp(keywords[k], "ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k], "line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k], "tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k], "body") != 0) continue;
return styles[k]->pack_data_bonus(buf,flag);
return styles[k]->pack_data_bonus(buf, flag);
}
return 0;
}
@ -493,12 +423,12 @@ int AtomVecHybrid::pack_data_bonus(double *buf, int flag)
void AtomVecHybrid::write_data_bonus(FILE *fp, int n, double *buf, int flag)
{
for (int k = 0; k < nstyles; k++) {
if (flag == ELLIPSOID && strcmp(keywords[k],"ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k],"line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k],"tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k],"body") != 0) continue;
if (flag == ELLIPSOID && strcmp(keywords[k], "ellipsoid") != 0) continue;
if (flag == LINE && strcmp(keywords[k], "line") != 0) continue;
if (flag == TRIANGLE && strcmp(keywords[k], "tri") != 0) continue;
if (flag == BODY && strcmp(keywords[k], "body") != 0) continue;
styles[k]->write_data_bonus(fp,n,buf,flag);
styles[k]->write_data_bonus(fp, n, buf, flag);
}
}
@ -508,11 +438,11 @@ void AtomVecHybrid::write_data_bonus(FILE *fp, int n, double *buf, int flag)
return -1 if name is unknown to any sub-styles
------------------------------------------------------------------------- */
int AtomVecHybrid::property_atom(char *name)
int AtomVecHybrid::property_atom(const std::string &name)
{
for (int k = 0; k < nstyles; k++) {
int index = styles[k]->property_atom(name);
if (index >= 0) return index*nstyles + k;
if (index >= 0) return index * nstyles + k;
}
return -1;
}
@ -522,12 +452,11 @@ int AtomVecHybrid::property_atom(char *name)
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
int nvalues, int groupbit)
void AtomVecHybrid::pack_property_atom(int multiindex, double *buf, int nvalues, int groupbit)
{
int k = multiindex % nstyles;
int index = multiindex/nstyles;
styles[k]->pack_property_atom(index,buf,nvalues,groupbit);
int index = multiindex / nstyles;
styles[k]->pack_property_atom(index, buf, nvalues, groupbit);
}
// ----------------------------------------------------------------------
@ -535,48 +464,21 @@ void AtomVecHybrid::pack_property_atom(int multiindex, double *buf,
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
merge fields and remove duplicate fields
concat = root + Inum fields string from all substyles
return dedup = concat with duplicate fields removed
merge fields into root vector and remove duplicate fields
if concat_flag set, also return concat (w/ duplicates)
so caller can check for problematic fields, call will free it
so caller can check for problematic fields
------------------------------------------------------------------------- */
char *AtomVecHybrid::merge_fields(int inum, char *root,
int concat_flag, char *&concat_str)
void AtomVecHybrid::merge_fields(std::vector<std::string> &root,
const std::vector<std::string> &fields, int concat_flag,
std::vector<std::string> &concat)
{
// create vector with all words combined
// grow vector with all words combined with dedup and
std::string concat;
if (root) concat += root;
for (int k = 0; k < nstyles; k++) {
if (concat.size() > 0) concat += " ";
concat += fieldstrings[k].fstr[inum];
for (const auto &field : fields) {
if (concat_flag) concat.push_back(field);
if (std::find(root.begin(), root.end(), field) == root.end()) root.push_back(field);
}
if (concat_flag) concat_str = utils::strdup(concat);
// remove duplicate words without changing the order
auto words = Tokenizer(concat, " ").as_vector();
std::vector<std::string> dedup;
for (auto &w : words) {
bool found = false;
for (auto &d : dedup) {
if (w == d) found = true;
}
if (!found) dedup.push_back(w);
}
// create final concatenated, deduped string
concat.clear();
for (auto &d : dedup) {
concat += d;
concat += " ";
}
// remove trailing blank
if (concat.size() > 0) concat.pop_back();
return utils::strdup(concat);
}
/* ----------------------------------------------------------------------
@ -587,19 +489,19 @@ void AtomVecHybrid::build_styles()
{
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#define AtomStyle(key, Class) nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle
#undef ATOM_CLASS
allstyles = new char*[nallstyles];
allstyles = new char *[nallstyles];
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
#define AtomStyle(key, Class) \
allstyles[nallstyles] = utils::strdup(#key); \
nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle
#undef ATOM_CLASS
}
@ -611,6 +513,6 @@ void AtomVecHybrid::build_styles()
int AtomVecHybrid::known_style(char *str)
{
for (int i = 0; i < nallstyles; i++)
if (strcmp(str,allstyles[i]) == 0) return 1;
if (strcmp(str, allstyles[i]) == 0) return 1;
return 0;
}

11
src/atom_vec_hybrid.h
View File

@ -64,23 +64,18 @@ class AtomVecHybrid : public AtomVec {
int pack_data_bonus(double *, int) override;
void write_data_bonus(FILE *, int, double *, int) override;
int property_atom(char *) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:
int nallstyles;
char **allstyles;
int fields_allocated;
struct FieldStrings {
char **fstr;
};
FieldStrings *fieldstrings;
int nstyles_bonus;
class AtomVec **styles_bonus;
char *merge_fields(int, char *, int, char *&);
void merge_fields(std::vector<std::string> &, const std::vector<std::string> &,
int, std::vector<std::string> &);
void build_styles();
int known_style(char *);
};

195
src/atom_vec_line.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -23,12 +22,11 @@
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
#define EPSILON 0.001
static constexpr double EPSILON = 0.001;
/* ---------------------------------------------------------------------- */
@ -55,18 +53,17 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "molecule radius rmass omega torque line";
fields_copy = (char *) "molecule radius rmass omega";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega";
fields_restart = (char *) "molecule radius rmass omega";
fields_create = (char *) "molecule radius rmass omega line";
fields_data_atom = (char *) "id molecule type line rmass x";
fields_data_vel = (char *) "id v omega";
fields_grow = {"molecule", "radius", "rmass", "omega", "torque", "line"};
fields_copy = {"molecule", "radius", "rmass", "omega"};
fields_comm_vel = {"omega"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega"};
fields_exchange = {"molecule", "radius", "rmass", "omega"};
fields_restart = {"molecule", "radius", "rmass", "omega"};
fields_create = {"molecule", "radius", "rmass", "omega", "line"};
fields_data_atom = {"id", "molecule", "type", "line", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
setup_fields();
}
@ -85,7 +82,7 @@ void AtomVecLine::init()
AtomVec::init();
if (domain->dimension != 2)
error->all(FLERR,"Atom_style line can only be used in 2d simulations");
error->all(FLERR, "Atom_style line can only be used in 2d simulations");
}
/* ----------------------------------------------------------------------
@ -108,11 +105,9 @@ void AtomVecLine::grow_pointers()
void AtomVecLine::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -124,7 +119,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && line[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,line[j]);
copy_bonus_all(nlocal_bonus - 1, line[j]);
nlocal_bonus--;
}
@ -143,7 +138,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
void AtomVecLine::copy_bonus_all(int i, int j)
{
line[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -164,7 +159,7 @@ void AtomVecLine::clear_bonus()
int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -179,7 +174,7 @@ int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -192,12 +187,13 @@ void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (line[j] < 0) buf[m++] = ubuf(0).d;
if (line[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
buf[m++] = bonus[line[j]].length;
@ -212,13 +208,14 @@ int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
int AtomVecLine::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
int i, j, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
if (line[i] == 0)
line[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -242,7 +239,8 @@ int AtomVecLine::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -260,7 +258,8 @@ int AtomVecLine::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -284,8 +283,10 @@ int AtomVecLine::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (line[i] >= 0) n += size_restart_bonus_one;
else n++;
if (line[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -301,7 +302,8 @@ int AtomVecLine::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (line[i] < 0) buf[m++] = ubuf(0).d;
if (line[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = line[i];
@ -321,7 +323,8 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
if (line[ilocal] == 0)
line[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].length = buf[m++];
@ -339,31 +342,32 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");
if (line[m]) error->one(FLERR, "Assigning line parameters to non-line atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
int ivalue = 1;
double x1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y1 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double y2 = utils::numeric(FLERR,values[ivalue++],true,lmp);
double x1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y1 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double x2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double y2 = utils::numeric(FLERR, values[ivalue++], true, lmp);
double dx = x2 - x1;
double dy = y2 - y1;
double length = sqrt(dx*dx + dy*dy);
double length = sqrt(dx * dx + dy * dy);
bonus[nlocal_bonus].length = length;
if (dy >= 0.0) bonus[nlocal_bonus].theta = acos(dx/length);
else bonus[nlocal_bonus].theta = -acos(dx/length);
if (dy >= 0.0)
bonus[nlocal_bonus].theta = acos(dx / length);
else
bonus[nlocal_bonus].theta = -acos(dx / length);
double xc = 0.5*(x1+x2);
double yc = 0.5*(y1+y2);
double xc = 0.5 * (x1 + x2);
double yc = 0.5 * (y1 + y2);
dx = xc - x[m][0];
dy = yc - x[m][1];
double delta = sqrt(dx*dx + dy*dy);
double delta = sqrt(dx * dx + dy * dy);
if (delta/length > EPSILON)
error->one(FLERR,"Inconsistent line segment in data file");
if (delta / length > EPSILON) error->one(FLERR, "Inconsistent line segment in data file");
x[m][0] = xc;
x[m][1] = yc;
@ -385,7 +389,7 @@ void AtomVecLine::data_atom_bonus(int m, const std::vector<std::string> &values)
double AtomVecLine::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -398,7 +402,7 @@ void AtomVecLine::create_atom_post(int ilocal)
{
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
line[ilocal] = -1;
}
@ -410,19 +414,22 @@ void AtomVecLine::create_atom_post(int ilocal)
void AtomVecLine::data_atom_post(int ilocal)
{
line_flag = line[ilocal];
if (line_flag == 0) line_flag = -1;
else if (line_flag == 1) line_flag = 0;
else error->one(FLERR,"Invalid line flag in Atoms section of data file");
if (line_flag == 0)
line_flag = -1;
else if (line_flag == 1)
line_flag = 0;
else
error->one(FLERR, "Invalid line flag in Atoms section of data file");
line[ilocal] = line_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
if (line_flag < 0) {
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
radius[ilocal] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -438,13 +445,16 @@ void AtomVecLine::pack_data_pre(int ilocal)
line_flag = line[ilocal];
rmass_one = rmass[ilocal];
if (line_flag < 0) line[ilocal] = 0;
else line[ilocal] = 1;
if (line_flag < 0)
line[ilocal] = 0;
else
line[ilocal] = 1;
if (line_flag < 0) {
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else rmass[ilocal] /= bonus[line_flag].length;
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
rmass[ilocal] /= bonus[line_flag].length;
}
/* ----------------------------------------------------------------------
@ -464,9 +474,9 @@ void AtomVecLine::pack_data_post(int ilocal)
int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
double length,theta;
double xc,yc,x1,x2,y1,y2;
int i, j;
double length, theta;
double xc, yc, x1, x2, y1, y2;
double **x = atom->x;
tagint *tag = atom->tag;
@ -482,15 +492,16 @@ int AtomVecLine::pack_data_bonus(double *buf, int /*flag*/)
theta = bonus[j].theta;
xc = x[i][0];
yc = x[i][1];
x1 = xc - 0.5*cos(theta)*length;
y1 = yc - 0.5*sin(theta)*length;
x2 = xc + 0.5*cos(theta)*length;
y2 = yc + 0.5*sin(theta)*length;
x1 = xc - 0.5 * cos(theta) * length;
y1 = yc - 0.5 * sin(theta) * length;
x2 = xc + 0.5 * cos(theta) * length;
y2 = yc + 0.5 * sin(theta) * length;
buf[m++] = x1;
buf[m++] = y1;
buf[m++] = x2;
buf[m++] = y2;
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
}
@ -503,8 +514,8 @@ void AtomVecLine::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {}\n",ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4]);
fmt::print(fp, "{} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2], buf[i + 3],
buf[i + 4]);
i += size_data_bonus;
}
}
@ -525,10 +536,11 @@ void AtomVecLine::set_length(int i, double value)
bonus[nlocal_bonus].ilocal = i;
line[i] = nlocal_bonus++;
} else if (value == 0.0) {
copy_bonus_all(nlocal_bonus-1,line[i]);
copy_bonus_all(nlocal_bonus - 1, line[i]);
nlocal_bonus--;
line[i] = -1;
} else bonus[line[i]].length = value;
} else
bonus[line[i]].length = value;
// also set radius = half of length
// unless value = 0.0, then set diameter = 1.0
@ -536,40 +548,3 @@ void AtomVecLine::set_length(int i, double value)
radius[i] = 0.5 * value;
if (value == 0.0) radius[i] = 0.5;
}
/* ----------------------------------------------------------------------
check consistency of internal Bonus data structure
n = # of atoms in regular structure to check against
------------------------------------------------------------------------- */
/*
void AtomVecLine::consistency_check(int n, char *str)
{
int iflag = 0;
int count = 0;
for (int i = 0; i < n; i++) {
if (line[i] >= 0) {
count++;
if (line[i] >= nlocal_bonus) iflag++;
if (bonus[line[i]].ilocal != i) iflag++;
//if (comm->me == 1 && update->ntimestep == 873)
// printf("CCHK %s: %d %d: %d %d: %d %d\n",
// str,i,n,line[i],nlocal_bonus,bonus[line[i]].ilocal,iflag);
}
}
if (iflag) {
printf("BAD vecline ptrs: %s: %d %d: %d\n",str,comm->me,
update->ntimestep,iflag);
MPI_Abort(world,1);
}
if (count != nlocal_bonus) {
char msg[128];
printf("BAD vecline count: %s: %d %d: %d %d\n",
str,comm->me,update->ntimestep,count,nlocal_bonus);
MPI_Abort(world,1);
}
}
*/

61
src/atom_vec_sphere.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -21,8 +20,6 @@
#include "math_const.h"
#include "modify.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -34,26 +31,24 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
molecular = Atom::ATOMIC;
atom->sphere_flag = 1;
atom->radius_flag = atom->rmass_flag = atom->omega_flag =
atom->torque_flag = 1;
atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "radius rmass omega torque";
fields_copy = (char *) "radius rmass omega";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega";
fields_reverse = (char *) "torque";
fields_border = (char *) "radius rmass";
fields_border_vel = (char *) "radius rmass omega";
fields_exchange = (char *) "radius rmass omega";
fields_restart = (char *) "radius rmass omega";
fields_create = (char *) "radius rmass omega";
fields_data_atom = (char *) "id type radius rmass x";
fields_data_vel = (char *) "id v omega";
fields_grow = {"radius", "rmass", "omega", "torque"};
fields_copy = {"radius", "rmass", "omega"};
fields_comm_vel = {"omega"};
fields_reverse = {"torque"};
fields_border = {"radius", "rmass"};
fields_border_vel = {"radius", "rmass", "omega"};
fields_exchange = {"radius", "rmass", "omega"};
fields_restart = {"radius", "rmass", "omega"};
fields_create = {"radius", "rmass", "omega"};
fields_data_atom = {"id", "type", "radius", "rmass", "x"};
fields_data_vel = {"id", "v", "omega"};
}
/* ----------------------------------------------------------------------
@ -63,21 +58,19 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecSphere::process_args(int narg, char **arg)
{
if (narg != 0 && narg != 1)
error->all(FLERR,"Illegal atom_style sphere command");
if (narg != 0 && narg != 1) error->all(FLERR, "Illegal atom_style sphere command");
radvary = 0;
if (narg == 1) {
radvary = utils::numeric(FLERR,arg[0],true,lmp);
if (radvary < 0 || radvary > 1)
error->all(FLERR,"Illegal atom_style sphere command");
radvary = utils::numeric(FLERR, arg[0], true, lmp);
if (radvary < 0 || radvary > 1) error->all(FLERR, "Illegal atom_style sphere command");
}
// dynamic particle radius and mass must be communicated every step
if (radvary) {
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
fields_comm = {"radius", "rmass"};
fields_comm_vel = {"radius", "rmass", "omega"};
}
// delay setting up of fields until now
@ -94,11 +87,10 @@ void AtomVecSphere::init()
// check if optional radvary setting should have been set to 1
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"adapt") == 0) {
auto fix = dynamic_cast<FixAdapt *>( modify->fix[i]);
if (strcmp(modify->fix[i]->style, "adapt") == 0) {
auto fix = dynamic_cast<FixAdapt *>(modify->fix[i]);
if (fix->diamflag && radvary == 0)
error->all(FLERR,"Fix adapt changes particle radii "
"but atom_style sphere is not dynamic");
error->all(FLERR, "Fix adapt changes particle radii but atom_style sphere is not dynamic");
}
}
@ -121,7 +113,7 @@ void AtomVecSphere::grow_pointers()
void AtomVecSphere::create_atom_post(int ilocal)
{
radius[ilocal] = 0.5;
rmass[ilocal] = 4.0*MY_PI/3.0 * 0.5*0.5*0.5;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * 0.5 * 0.5 * 0.5;
}
/* ----------------------------------------------------------------------
@ -133,11 +125,9 @@ void AtomVecSphere::data_atom_post(int ilocal)
{
radius_one = 0.5 * atom->radius[ilocal];
radius[ilocal] = radius_one;
if (radius_one > 0.0)
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
if (radius_one > 0.0) rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -154,9 +144,8 @@ void AtomVecSphere::pack_data_pre(int ilocal)
rmass_one = rmass[ilocal];
radius[ilocal] *= 2.0;
if (radius_one!= 0.0)
rmass[ilocal] =
rmass_one / (4.0*MY_PI/3.0 * radius_one*radius_one*radius_one);
if (radius_one != 0.0)
rmass[ilocal] = rmass_one / (4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one);
}
/* ----------------------------------------------------------------------

262
src/atom_vec_tri.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -19,18 +18,17 @@
#include "error.h"
#include "fix.h"
#include "math_const.h"
#include "math_extra.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
using MathConst::MY_PI;
#define EPSILON 0.001
static constexpr double EPSILON = 0.001;
/* ---------------------------------------------------------------------- */
@ -58,18 +56,17 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "molecule radius rmass omega angmom torque tri";
fields_copy = (char *) "molecule radius rmass omega angmom";
fields_comm = (char *) "";
fields_comm_vel = (char *) "omega angmom";
fields_reverse = (char *) "torque";
fields_border = (char *) "molecule radius rmass";
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega angmom";
fields_restart = (char *) "molecule radius rmass omega angmom";
fields_create = (char *) "molecule radius rmass omega angmom tri";
fields_data_atom = (char *) "id molecule type tri rmass x";
fields_data_vel = (char *) "id v omega angmom";
fields_grow = {"molecule", "radius", "rmass", "omega", "angmom", "torque", "tri"};
fields_copy = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_comm_vel = {"omega", "angmom"};
fields_reverse = {"torque"};
fields_border = {"molecule", "radius", "rmass"};
fields_border_vel = {"molecule", "radius", "rmass", "omega"};
fields_exchange = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_restart = {"molecule", "radius", "rmass", "omega", "angmom"};
fields_create = {"molecule", "radius", "rmass", "omega", "angmom", "tri"};
fields_data_atom = {"id", "molecule", "type", "tri", "rmass", "x"};
fields_data_vel = {"id", "v", "omega", "angmom"};
setup_fields();
}
@ -88,7 +85,7 @@ void AtomVecTri::init()
AtomVec::init();
if (domain->dimension != 3)
error->all(FLERR,"Atom_style tri can only be used in 3d simulations");
error->all(FLERR, "Atom_style tri can only be used in 3d simulations");
}
/* ----------------------------------------------------------------------
@ -112,11 +109,9 @@ void AtomVecTri::grow_pointers()
void AtomVecTri::grow_bonus()
{
nmax_bonus = grow_nmax_bonus(nmax_bonus);
if (nmax_bonus < 0)
error->one(FLERR,"Per-processor system is too big");
if (nmax_bonus < 0) error->one(FLERR, "Per-processor system is too big");
bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
"atom:bonus");
bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "atom:bonus");
}
/* ----------------------------------------------------------------------
@ -129,7 +124,7 @@ void AtomVecTri::copy_bonus(int i, int j, int delflag)
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && tri[j] >= 0) {
copy_bonus_all(nlocal_bonus-1,tri[j]);
copy_bonus_all(nlocal_bonus - 1, tri[j]);
nlocal_bonus--;
}
@ -148,7 +143,7 @@ void AtomVecTri::copy_bonus(int i, int j, int delflag)
void AtomVecTri::copy_bonus_all(int i, int j)
{
tri[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
memcpy(&bonus[j], &bonus[i], sizeof(Bonus));
}
/* ----------------------------------------------------------------------
@ -169,7 +164,7 @@ void AtomVecTri::clear_bonus()
int AtomVecTri::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
double *quat;
m = 0;
@ -191,7 +186,7 @@ int AtomVecTri::pack_comm_bonus(int n, int *list, double *buf)
void AtomVecTri::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
double *quat;
m = 0;
@ -211,13 +206,14 @@ void AtomVecTri::unpack_comm_bonus(int n, int first, double *buf)
int AtomVecTri::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*c1,*c2,*c3,*inertia;
int i, j, m;
double *quat, *c1, *c2, *c3, *inertia;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
if (tri[j] < 0) buf[m++] = ubuf(0).d;
if (tri[j] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
quat = bonus[tri[j]].quat;
@ -251,14 +247,15 @@ int AtomVecTri::pack_border_bonus(int n, int *list, double *buf)
int AtomVecTri::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
int i, j, m, last;
double *quat, *c1, *c2, *c3, *inertia;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
if (tri[i] == 0)
tri[i] = -1;
else {
j = nlocal_bonus + nghost_bonus;
if (j == nmax_bonus) grow_bonus();
@ -301,7 +298,8 @@ int AtomVecTri::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
if (tri[i] < 0) buf[m++] = ubuf(0).d;
if (tri[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
@ -338,7 +336,8 @@ int AtomVecTri::unpack_exchange_bonus(int ilocal, double *buf)
int m = 0;
tri[ilocal] = (int) ubuf(buf[m++]).i;
if (tri[ilocal] == 0) tri[ilocal] = -1;
if (tri[ilocal] == 0)
tri[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -381,8 +380,10 @@ int AtomVecTri::size_restart_bonus()
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (tri[i] >= 0) n += size_restart_bonus_one;
else n++;
if (tri[i] >= 0)
n += size_restart_bonus_one;
else
n++;
}
return n;
@ -396,7 +397,8 @@ int AtomVecTri::pack_restart_bonus(int i, double *buf)
{
int m = 0;
if (tri[i] < 0) buf[m++] = ubuf(0).d;
if (tri[i] < 0)
buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
int j = tri[i];
@ -435,7 +437,8 @@ int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
int m = 0;
tri[ilocal] = (int) ubuf(buf[m++]).i;
if (tri[ilocal] == 0) tri[ilocal] = -1;
if (tri[ilocal] == 0)
tri[ilocal] = -1;
else {
if (nlocal_bonus == nmax_bonus) grow_bonus();
double *quat = bonus[nlocal_bonus].quat;
@ -472,52 +475,51 @@ int AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
{
if (tri[m]) error->one(FLERR,"Assigning tri parameters to non-tri atom");
if (tri[m]) error->one(FLERR, "Assigning tri parameters to non-tri atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
double c1[3],c2[3],c3[3];
double c1[3], c2[3], c3[3];
int ivalue = 1;
c1[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c2[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[0] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[1] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c3[2] = utils::numeric(FLERR,values[ivalue++],true,lmp);
c1[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c1[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c1[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c2[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
c3[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
// check for duplicate points
if (c1[0] == c2[0] && c1[1] == c2[1] && c1[2] == c2[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
if (c1[0] == c3[0] && c1[1] == c3[1] && c1[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
if (c2[0] == c3[0] && c2[1] == c3[1] && c2[2] == c3[2])
error->one(FLERR,"Invalid shape in Triangles section of data file");
error->one(FLERR, "Invalid shape in Triangles section of data file");
// size = length of one edge
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double size = MAX(MathExtra::len3(c2mc1),MathExtra::len3(c3mc1));
double c2mc1[3], c3mc1[3];
MathExtra::sub3(c2, c1, c2mc1);
MathExtra::sub3(c3, c1, c3mc1);
double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1));
// centroid = 1/3 of sum of vertices
double centroid[3];
centroid[0] = (c1[0]+c2[0]+c3[0]) / 3.0;
centroid[1] = (c1[1]+c2[1]+c3[1]) / 3.0;
centroid[2] = (c1[2]+c2[2]+c3[2]) / 3.0;
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
double dx = centroid[0] - x[m][0];
double dy = centroid[1] - x[m][1];
double dz = centroid[2] - x[m][2];
double delta = sqrt(dx*dx + dy*dy + dz*dz);
double delta = sqrt(dx * dx + dy * dy + dz * dz);
if (delta/size > EPSILON)
error->one(FLERR,"Inconsistent triangle in data file");
if (delta / size > EPSILON) error->one(FLERR, "Inconsistent triangle in data file");
x[m][0] = centroid[0];
x[m][1] = centroid[1];
@ -528,29 +530,29 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
// tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex
double c4[3];
MathExtra::sub3(c1,centroid,c4);
MathExtra::sub3(c1, centroid, c4);
radius[m] = MathExtra::lensq3(c4);
MathExtra::sub3(c2,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
MathExtra::sub3(c3,centroid,c4);
radius[m] = MAX(radius[m],MathExtra::lensq3(c4));
MathExtra::sub3(c2, centroid, c4);
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
MathExtra::sub3(c3, centroid, c4);
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
radius[m] = sqrt(radius[m]);
double norm[3];
MathExtra::cross3(c2mc1,c3mc1,norm);
MathExtra::cross3(c2mc1, c3mc1, norm);
double area = 0.5 * MathExtra::len3(norm);
rmass[m] *= area;
// inertia = inertia tensor of triangle as 6-vector in Voigt ordering
double inertia[6];
MathExtra::inertia_triangle(c1,c2,c3,rmass[m],inertia);
MathExtra::inertia_triangle(c1, c2, c3, rmass[m], inertia);
// diagonalize inertia tensor via Jacobi rotations
// bonus[].inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy_space = 3 evectors = principal axes of triangle
double tensor[3][3],evectors[3][3];
double tensor[3][3], evectors[3][3];
tensor[0][0] = inertia[0];
tensor[1][1] = inertia[1];
tensor[2][2] = inertia[2];
@ -558,10 +560,10 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
tensor[0][2] = tensor[2][0] = inertia[4];
tensor[0][1] = tensor[1][0] = inertia[5];
int ierror = MathEigen::jacobi3(tensor,bonus[nlocal_bonus].inertia,evectors);
if (ierror) error->one(FLERR,"Insufficient Jacobi rotations for triangle");
int ierror = MathEigen::jacobi3(tensor, bonus[nlocal_bonus].inertia, evectors);
if (ierror) error->one(FLERR, "Insufficient Jacobi rotations for triangle");
double ex_space[3],ey_space[3],ez_space[3];
double ex_space[3], ey_space[3], ez_space[3];
ex_space[0] = evectors[0][0];
ex_space[1] = evectors[1][0];
ex_space[2] = evectors[2][0];
@ -575,26 +577,23 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
// enforce 3 orthogonal vectors as a right-handed coordinate system
// flip 3rd vector if needed
MathExtra::cross3(ex_space,ey_space,norm);
if (MathExtra::dot3(norm,ez_space) < 0.0) MathExtra::negate3(ez_space);
MathExtra::cross3(ex_space, ey_space, norm);
if (MathExtra::dot3(norm, ez_space) < 0.0) MathExtra::negate3(ez_space);
// create initial quaternion
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus[nlocal_bonus].quat);
MathExtra::exyz_to_q(ex_space, ey_space, ez_space, bonus[nlocal_bonus].quat);
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
// in basis of principal axes
double disp[3];
MathExtra::sub3(c1,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c1);
MathExtra::sub3(c2,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c2);
MathExtra::sub3(c3,centroid,disp);
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
disp,bonus[nlocal_bonus].c3);
MathExtra::sub3(c1, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c1);
MathExtra::sub3(c2, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c2);
MathExtra::sub3(c3, centroid, disp);
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c3);
bonus[nlocal_bonus].ilocal = m;
tri[m] = nlocal_bonus++;
@ -607,7 +606,7 @@ void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
double AtomVecTri::memory_usage_bonus()
{
double bytes = 0;
bytes += (double)nmax_bonus*sizeof(Bonus);
bytes += (double) nmax_bonus * sizeof(Bonus);
return bytes;
}
@ -620,7 +619,7 @@ void AtomVecTri::create_atom_post(int ilocal)
{
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
tri[ilocal] = -1;
}
@ -632,19 +631,22 @@ void AtomVecTri::create_atom_post(int ilocal)
void AtomVecTri::data_atom_post(int ilocal)
{
tri_flag = tri[ilocal];
if (tri_flag == 0) tri_flag = -1;
else if (tri_flag == 1) tri_flag = 0;
else error->one(FLERR,"Invalid tri flag in Atoms section of data file");
if (tri_flag == 0)
tri_flag = -1;
else if (tri_flag == 1)
tri_flag = 0;
else
error->one(FLERR, "Invalid tri flag in Atoms section of data file");
tri[ilocal] = tri_flag;
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
if (tri_flag < 0) {
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else
radius[ilocal] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
@ -663,17 +665,19 @@ void AtomVecTri::pack_data_pre(int ilocal)
tri_flag = tri[ilocal];
rmass_one = rmass[ilocal];
if (tri_flag < 0) tri[ilocal] = 0;
else tri[ilocal] = 1;
if (tri_flag < 0)
tri[ilocal] = 0;
else
tri[ilocal] = 1;
if (tri_flag < 0) {
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
} else {
double c2mc1[3],c3mc1[3],norm[3];
MathExtra::sub3(bonus[tri_flag].c2,bonus[tri_flag].c1,c2mc1);
MathExtra::sub3(bonus[tri_flag].c3,bonus[tri_flag].c1,c3mc1);
MathExtra::cross3(c2mc1,c3mc1,norm);
double c2mc1[3], c3mc1[3], norm[3];
MathExtra::sub3(bonus[tri_flag].c2, bonus[tri_flag].c1, c2mc1);
MathExtra::sub3(bonus[tri_flag].c3, bonus[tri_flag].c1, c3mc1);
MathExtra::cross3(c2mc1, c3mc1, norm);
double area = 0.5 * MathExtra::len3(norm);
rmass[ilocal] /= area;
}
@ -696,9 +700,9 @@ void AtomVecTri::pack_data_post(int ilocal)
int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
{
int i,j;
double xc,yc,zc;
double dc1[3],dc2[3],dc3[3];
int i, j;
double xc, yc, zc;
double dc1[3], dc2[3], dc3[3];
double p[3][3];
double **x = atom->x;
@ -711,10 +715,10 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
if (buf) {
buf[m++] = ubuf(tag[i]).d;
j = tri[i];
MathExtra::quat_to_mat(bonus[j].quat,p);
MathExtra::matvec(p,bonus[j].c1,dc1);
MathExtra::matvec(p,bonus[j].c2,dc2);
MathExtra::matvec(p,bonus[j].c3,dc3);
MathExtra::quat_to_mat(bonus[j].quat, p);
MathExtra::matvec(p, bonus[j].c1, dc1);
MathExtra::matvec(p, bonus[j].c2, dc2);
MathExtra::matvec(p, bonus[j].c3, dc3);
xc = x[i][0];
yc = x[i][1];
zc = x[i][2];
@ -727,7 +731,8 @@ int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
buf[m++] = xc + dc3[0];
buf[m++] = yc + dc3[1];
buf[m++] = zc + dc3[2];
} else m += size_data_bonus;
} else
m += size_data_bonus;
}
return m;
}
@ -740,9 +745,8 @@ void AtomVecTri::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
{
int i = 0;
while (i < n) {
fmt::print(fp,"{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i,
buf[i+1],buf[i+2],buf[i+3],buf[i+4],buf[i+5],buf[i+6],
buf[i+7],buf[i+8],buf[i+9]);
fmt::print(fp, "{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2],
buf[i + 3], buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7], buf[i + 8], buf[i + 9]);
i += size_data_bonus;
}
}
@ -770,24 +774,24 @@ void AtomVecTri::set_equilateral(int i, double size)
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = 0.0;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[0] = -size / 2.0;
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[0] = size / 2.0;
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
radius[i] = MathExtra::len3(c1);
bonus[nlocal_bonus].ilocal = i;
tri[i] = nlocal_bonus++;
} else if (size == 0.0) {
radius[i] = 0.5;
copy_bonus_all(nlocal_bonus-1,tri[i]);
copy_bonus_all(nlocal_bonus - 1, tri[i]);
nlocal_bonus--;
tri[i] = -1;
} else {
@ -795,18 +799,18 @@ void AtomVecTri::set_equilateral(int i, double size)
double *c2 = bonus[tri[i]].c2;
double *c3 = bonus[tri[i]].c3;
double *inertia = bonus[tri[i]].inertia;
c1[0] = -size/2.0;
c1[1] = -sqrt(3.0)/2.0 * size / 3.0;
c1[0] = -size / 2.0;
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c1[2] = 0.0;
c2[0] = size/2.0;
c2[1] = -sqrt(3.0)/2.0 * size / 3.0;
c2[0] = size / 2.0;
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
c2[2] = 0.0;
c3[0] = 0.0;
c3[1] = sqrt(3.0)/2.0 * size * 2.0/3.0;
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
c3[2] = 0.0;
inertia[0] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[1] = sqrt(3.0)/96.0 * size*size*size*size;
inertia[2] = sqrt(3.0)/48.0 * size*size*size*size;
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
radius[i] = MathExtra::len3(c1);
}
}

7
src/bond.cpp
View File

@ -43,6 +43,7 @@ Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp)
energy = 0.0;
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
writedata = 1;
reinitflag = 1;
comm_forward = comm_reverse = comm_reverse_off = 0;
@ -337,11 +338,13 @@ double Bond::memory_usage()
}
/* -----------------------------------------------------------------------
Reset all type-based bond params via init.
reset all type-based bond params via init()
-------------------------------------------------------------------------- */
void Bond::reinit()
{
if (!reinitflag) error->all(FLERR, "Fix adapt interface to this bond style not supported");
if (!reinitflag)
error->all(FLERR, "Fix adapt interface to this bond style not supported");
init();
}

6
src/bond.h
View File

@ -39,7 +39,8 @@ class Bond : protected Pointers {
int comm_reverse; // size of reverse communication (0 if none)
int comm_reverse_off; // size of reverse comm even if newton off
int reinitflag; // 1 if compatible with fix adapt and alike
int reinitflag; // 0 if not compatible with fix adapt
// extract() method may still need to be added
// KOKKOS host/device flag and data masks
@ -63,7 +64,8 @@ class Bond : protected Pointers {
virtual double single(int, double, int, int, double &) = 0;
virtual double memory_usage();
virtual void *extract(const char *, int &) { return nullptr; }
virtual void reinit();
void reinit();
virtual int pack_forward_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_forward_comm(int, int, double *) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}

2
src/compute.h
View File

@ -108,7 +108,7 @@ class Compute : protected Pointers {
Compute(class LAMMPS *, int, char **);
~Compute() override;
void modify_params(int, char **);
void reset_extra_dof();
virtual void reset_extra_dof();
virtual void init() = 0;
virtual void init_list(int, class NeighList *) {}

61
src/compute_cluster_atom.cpp
View File

@ -30,8 +30,6 @@
using namespace LAMMPS_NS;
enum { CLUSTER, MASK, COORDS };
/* ---------------------------------------------------------------------- */
ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
@ -44,7 +42,7 @@ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom_cols = 0;
comm_forward = 3;
comm_forward = 1;
nmax = 0;
}
@ -117,22 +115,6 @@ void ComputeClusterAtom::compute_peratom()
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// if update->post_integrate set:
// a dynamic group in FixGroup is invoking a variable with this compute
// thus ghost atom coords need to be up-to-date after initial_integrate()
if (update->post_integrate) {
commflag = COORDS;
comm->forward_comm(this);
}
// if group is dynamic, insure ghost atom masks are current
if (group->dynamic[igroup]) {
commflag = MASK;
comm->forward_comm(this);
}
// every atom starts in its own cluster, with clusterID = atomID
tagint *tag = atom->tag;
@ -153,7 +135,6 @@ void ComputeClusterAtom::compute_peratom()
// iterate until no changes in my atoms
// then check if any proc made changes
commflag = CLUSTER;
double **x = atom->x;
int change, done, anychange;
@ -203,31 +184,15 @@ void ComputeClusterAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int i, j, m;
m = 0;
if (commflag == CLUSTER) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = clusterID[j];
}
} else if (commflag == MASK) {
int *mask = atom->mask;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(mask[j]).d;
}
} else if (commflag == COORDS) {
double **x = atom->x;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = clusterID[j];
}
return m;
@ -241,19 +206,7 @@ void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
m = 0;
last = first + n;
if (commflag == CLUSTER) {
for (i = first; i < last; i++) clusterID[i] = buf[m++];
} else if (commflag == MASK) {
int *mask = atom->mask;
for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
} else if (commflag == COORDS) {
double **x = atom->x;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
for (i = first; i < last; i++) clusterID[i] = buf[m++];
}
/* ----------------------------------------------------------------------

22
src/compute_coord_atom.cpp
View File

@ -259,14 +259,16 @@ void ComputeCoordAtom::compute_peratom()
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
for (m = 0; m < ncol; m++)
if (jtype >= typelo[m] && jtype <= typehi[m]) count[m] += 1.0;
if (mask[j] & jgroupbit) {
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
for (m = 0; m < ncol; m++)
if (jtype >= typelo[m] && jtype <= typehi[m]) count[m] += 1.0;
}
}
}
}
@ -309,8 +311,8 @@ void ComputeCoordAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int i, m = 0, j;
for (i = 0; i < n; ++i) {

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