forked from lijiext/lammps
Merge branch 'tokenizer' of github.com:rbberger/lammps into tokenizer
This commit is contained in:
Richard Berger
commit
1889b165dc
|
|
@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
|
|||
``cmake .`` and then compile again. The included dependency tracking
|
||||
should make certain that only the necessary subset of files are
|
||||
re-compiled. You can also delete compiled objects, libraries and
|
||||
executables with ``cmake --build . clean`` (or ``make clean``).
|
||||
executables with ``cmake --build . --target clean`` (or ``make clean``).
|
||||
|
||||
After compilation, you may optionally install the LAMMPS executable into
|
||||
your system with:
|
||||
|
|
|
|||
|
|
@ -75,9 +75,9 @@ The unit testing facility is integrated into the CMake build process
|
|||
of the LAMMPS source code distribution itself. It can be enabled by
|
||||
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
|
||||
It requires the `YAML <http://pyyaml.org/>`_ library and development
|
||||
headers to compile and will download and compile the
|
||||
headers to compile and will download and compile a recent version of the
|
||||
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
|
||||
for programming the tests.
|
||||
for implementing the tests.
|
||||
|
||||
After compilation is complete, the unit testing is started in the build
|
||||
folder using the ``ctest`` command, which is part of the CMake software.
|
||||
|
|
@ -100,6 +100,30 @@ The output of this command will be looking something like this::
|
|||
|
||||
Total Test time (real) = 0.27 sec
|
||||
|
||||
|
||||
The ``ctest`` command has many options, the most important ones are:
|
||||
|
||||
.. list-table::
|
||||
|
||||
* - Option
|
||||
- Function
|
||||
* - -V
|
||||
- verbose output: display output of individual test runs
|
||||
* - -j <num>
|
||||
- parallel run: run <num> tests in parallel
|
||||
* - -R <regex>
|
||||
- run subset of tests matching the regular expression <regex>
|
||||
* - -E <regex>
|
||||
- exclude subset of tests matching the regular expression <regex>
|
||||
* - -N
|
||||
- dry-run: display list of tests without running them
|
||||
|
||||
In its full implementation, the unit test framework will consist of multiple
|
||||
kinds of tests implemented in different programming languages (C++, C, Python,
|
||||
Fortran) and testing different aspects of the LAMMPS software and its features.
|
||||
At the moment only tests for "force styles" are implemented. More on those
|
||||
in the next section.
|
||||
|
||||
.. note::
|
||||
|
||||
This unit test framework is new and still under development.
|
||||
|
|
@ -114,6 +138,112 @@ The output of this command will be looking something like this::
|
|||
the contents of the YAML files for existing test programs
|
||||
will be provided in time as well.
|
||||
|
||||
Unit tests for force styles
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
A large part of LAMMPS are different "styles" for computing non-bonded
|
||||
and bonded interactions selected through the :doc:`pair_style`,
|
||||
:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
|
||||
:doc:`improper_style`, and :doc:`kspace_style`. Since these all share
|
||||
common interfaces, it is possible to write generic test programs that
|
||||
will call those common interfaces for small test systems with less than
|
||||
100 atoms and compare the results with pre-recorded reference results.
|
||||
A test run is then a a collection multiple individual test runs each
|
||||
with many comparisons to reference results based on template input
|
||||
files, individual command settings, relative error margins, and
|
||||
reference data stored in a YAML format file with ``.yaml``
|
||||
suffix. Currently the programs ``pair_style``, ``bond_style``, and
|
||||
``angle_style`` are implemented. They will compare forces, energies and
|
||||
(global) stress for all atoms after a ``run 0`` calculation and after a
|
||||
few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
|
||||
with different settings and also for multiple accelerated styles. If a
|
||||
prerequisite style or package is missing, the individual tests are
|
||||
skipped. All tests will be executed on a single MPI process, so using
|
||||
the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
|
||||
since this will skip the MPI initialization for each test run.
|
||||
Below is an example command and output:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
[tests]$ pair_style mol-pair-lj_cut.yaml
|
||||
[==========] Running 6 tests from 1 test suite.
|
||||
[----------] Global test environment set-up.
|
||||
[----------] 6 tests from PairStyle
|
||||
[ RUN ] PairStyle.plain
|
||||
[ OK ] PairStyle.plain (24 ms)
|
||||
[ RUN ] PairStyle.omp
|
||||
[ OK ] PairStyle.omp (18 ms)
|
||||
[ RUN ] PairStyle.intel
|
||||
[ OK ] PairStyle.intel (6 ms)
|
||||
[ RUN ] PairStyle.opt
|
||||
[ SKIPPED ] PairStyle.opt (0 ms)
|
||||
[ RUN ] PairStyle.single
|
||||
[ OK ] PairStyle.single (7 ms)
|
||||
[ RUN ] PairStyle.extract
|
||||
[ OK ] PairStyle.extract (6 ms)
|
||||
[----------] 6 tests from PairStyle (62 ms total)
|
||||
|
||||
[----------] Global test environment tear-down
|
||||
[==========] 6 tests from 1 test suite ran. (63 ms total)
|
||||
[ PASSED ] 5 tests.
|
||||
[ SKIPPED ] 1 test, listed below:
|
||||
[ SKIPPED ] PairStyle.opt
|
||||
|
||||
In this particular case, 5 out of 6 sets of tests were conducted, the
|
||||
tests for the ``lj/cut/opt`` pair style was skipped, since the tests
|
||||
executable did not include it. To learn what individual tests are performed,
|
||||
you (currently) need to read the source code. You can use code coverage
|
||||
recording (see next section) to confirm how well the tests cover the individual
|
||||
source files.
|
||||
|
||||
The force style test programs have a common set of options:
|
||||
|
||||
.. list-table::
|
||||
|
||||
* - Option
|
||||
- Function
|
||||
* - -g <newfile>
|
||||
- regenerate reference data in new YAML file
|
||||
* - -u
|
||||
- update reference data in the original YAML file
|
||||
* - -s
|
||||
- print error statistics for each group of comparisons
|
||||
* - -v
|
||||
- verbose output: also print the executed LAMMPS commands
|
||||
|
||||
To add a test for a style that is not yet covered, it is usually best
|
||||
to copy a YAML file for a similar style to a new file, edit the details
|
||||
of the style (how to call it, how to set its coefficients) and then
|
||||
run test command with either the *-g* and the replace the initial
|
||||
test file with the regenerated one or the *-u* option. The *-u* option
|
||||
will destroy the original file, if the generation run does not complete,
|
||||
so using *-g* is recommended unless the YAML file is fully tested
|
||||
and working.
|
||||
|
||||
.. admonition:: Recommendations and notes for YAML files
|
||||
:class: note
|
||||
|
||||
- The reference results should be recorded without any code
|
||||
optimization or related compiler flags enabled.
|
||||
- The ``epsilon`` parameter defines the relative precision with which
|
||||
the reference results must be met. The test geometries often have
|
||||
high and low energy parts and thus a significant impact from
|
||||
floating-point math truncation errors is to be expected. Some
|
||||
functional forms and potentials are more noisy than others, so this
|
||||
parameter needs to be adjusted. Typically a value around 1.0e-13
|
||||
can be used, but it may need to be as large as 1.0e-8 in some
|
||||
cases.
|
||||
- The tests for pair styles from OPT, USER-OMP and USER-INTEL are
|
||||
performed with automatically rescaled epsilon to account for
|
||||
additional loss of precision from code optimizations and different
|
||||
summation orders.
|
||||
- When compiling with aggressive compiler optimization, some tests
|
||||
are likely to fail. It is recommended to inspect the individual
|
||||
tests in detail to decide whether the specific error for a specific
|
||||
property is acceptable (it often is), or this may be an indication
|
||||
of mis-compiled code (or undesired large of precision due to
|
||||
reordering of operations).
|
||||
|
||||
------------
|
||||
|
||||
You can also collect code coverage metrics while running the tests by
|
||||
|
|
|
|||
|
|
@ -415,8 +415,10 @@ This is particularly convenient, if you have set a custom build command
|
|||
via the ``CMAKE_MAKE_PROGRAM`` variable.
|
||||
|
||||
When calling the build program, you can also select which "target" is to
|
||||
be build through appending the name of the target to the build command.
|
||||
Example: ``cmake --build . all``. The following abstract targets are available:
|
||||
be build through appending the ``--target`` flag and the name of the target
|
||||
to the build command. When using ``make`` as build tool, you can just append
|
||||
the target name to the command. Example: ``cmake --build . --target all`` or
|
||||
``make all``. The following abstract targets are available:
|
||||
|
||||
.. list-table::
|
||||
:header-rows: 1
|
||||
|
|
@ -432,7 +434,7 @@ Example: ``cmake --build . all``. The following abstract targets are available:
|
|||
* - ``install``
|
||||
- install all target files into folders in ``CMAKE_INSTALL_PREFIX``
|
||||
* - ``test``
|
||||
- run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
|
||||
- run some tests (if configured with ``-D ENABLE_TESTING=on``)
|
||||
* - ``clean``
|
||||
- remove all generated files
|
||||
|
||||
|
|
|
|||
|
|
@ -1985,6 +1985,7 @@ Neumann
|
|||
Nevent
|
||||
nevery
|
||||
Nevery
|
||||
newfile
|
||||
Newns
|
||||
newtype
|
||||
Neyts
|
||||
|
|
|
|||
|
|
@ -464,7 +464,8 @@ void kimProperty::command(int narg, char **arg)
|
|||
error->one(FLERR, "Error Python `kim_property_dump` function "
|
||||
"evaluation failed!");
|
||||
}
|
||||
}
|
||||
} else
|
||||
pValue = NULL;
|
||||
|
||||
// Destroy the variable
|
||||
kim_str_cmd[1] = const_cast<char *>("delete");
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -91,6 +91,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -91,6 +91,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -98,6 +98,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -102,6 +102,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -109,6 +109,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -94,6 +94,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -112,6 +112,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -99,6 +99,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -96,6 +96,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -95,6 +95,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -96,6 +96,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -94,6 +94,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -98,6 +98,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -96,6 +96,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -96,6 +96,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -95,6 +95,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -97,6 +97,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -93,6 +93,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -94,6 +94,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -92,6 +92,7 @@ $(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
|
|||
# Library targets
|
||||
|
||||
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
|
||||
@rm -f ../$(ARLIB)
|
||||
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
|
||||
@rm -f $(ARLIB)
|
||||
@ln -s ../$(ARLIB) $(ARLIB)
|
||||
|
|
|
|||
|
|
@ -33,7 +33,8 @@ enum{SCALAR,VECTOR,ARRAY};
|
|||
|
||||
ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
|
||||
radelem(NULL), wjelem(NULL), snap_peratom(NULL), snapall(NULL)
|
||||
snapall(NULL), snap_peratom(NULL), radelem(NULL), wjelem(NULL),
|
||||
snaptr(NULL)
|
||||
{
|
||||
|
||||
array_flag = 1;
|
||||
|
|
@ -41,9 +42,6 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
double rfac0, rmin0;
|
||||
int twojmax, switchflag, bzeroflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
int ntypes = atom->ntypes;
|
||||
int nargmin = 6+2*ntypes;
|
||||
|
||||
|
|
@ -413,7 +411,6 @@ void ComputeSnap::compute_array()
|
|||
const int typeoffset_local = ndims_peratom*nperdim*itype;
|
||||
const int typeoffset_global = nperdim*itype;
|
||||
for (int icoeff = 0; icoeff < nperdim; icoeff++) {
|
||||
int irow = 1;
|
||||
for (int i = 0; i < ntotal; i++) {
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
int iglobal = atom->tag[i];
|
||||
|
|
|
|||
|
|
@ -112,7 +112,6 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
|
|||
double theta1,t1dir[3],cost1;
|
||||
double theta2,t2dir[3],cost2;
|
||||
double theta3,t3dir[3],cost3;
|
||||
double theta4,theta4p,t4dir[3],cost4;
|
||||
double theta7,theta7p,t7dir[3],cost7;
|
||||
double theta8,theta8p,t8dir[3],cost8;
|
||||
|
||||
|
|
|
|||
|
|
@ -256,7 +256,7 @@ void ComputeViscosityCos::remove_bias_all() {
|
|||
assume remove_bias() was previously called
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::restore_bias(int i, double *v) {
|
||||
void ComputeViscosityCos::restore_bias(int /* i */, double *v) {
|
||||
v[0] += vbias[0];
|
||||
v[1] += vbias[1];
|
||||
v[2] += vbias[2];
|
||||
|
|
@ -267,7 +267,7 @@ void ComputeViscosityCos::restore_bias(int i, double *v) {
|
|||
assume remove_bias_thr() was previously called with the same buffer b
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeViscosityCos::restore_bias_thr(int i, double *v, double *b) {
|
||||
void ComputeViscosityCos::restore_bias_thr(int /* i */, double *v, double *b) {
|
||||
v[0] += b[0];
|
||||
v[1] += b[1];
|
||||
v[2] += b[2];
|
||||
|
|
|
|||
|
|
@ -58,7 +58,7 @@ void FixAccelerateCos::setup(int vflag) {
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixAccelerateCos::post_force(int vflag) {
|
||||
void FixAccelerateCos::post_force(int /* vflag */) {
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
|
|
|
|||
|
|
@ -1835,7 +1835,6 @@ void AtomVec::pack_data(double **buf)
|
|||
void AtomVec::write_data(FILE *fp, int n, double **buf)
|
||||
{
|
||||
int i,j,m,nn,datatype,cols;
|
||||
void *pdata;
|
||||
|
||||
for (i = 0; i < n; i++) {
|
||||
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
|
||||
|
|
@ -1984,40 +1983,32 @@ void AtomVec::pack_vel(double **buf)
|
|||
void AtomVec::write_vel(FILE *fp, int n, double **buf)
|
||||
{
|
||||
int i,j,m,nn,datatype,cols;
|
||||
void *pdata;
|
||||
|
||||
for (i = 0; i < n; i++) {
|
||||
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
|
||||
|
||||
j = 1;
|
||||
for (nn = 1; nn < ndata_vel; nn++) {
|
||||
pdata = mdata_vel.pdata[nn];
|
||||
datatype = mdata_vel.datatype[nn];
|
||||
cols = mdata_vel.cols[nn];
|
||||
if (datatype == DOUBLE) {
|
||||
if (cols == 0) {
|
||||
double *vec = *((double **) pdata);
|
||||
fprintf(fp," %-1.16e",buf[i][j++]);
|
||||
} else {
|
||||
double **array = *((double ***) pdata);
|
||||
for (m = 0; m < cols; m++)
|
||||
fprintf(fp," %-1.16e",buf[i][j++]);
|
||||
}
|
||||
} else if (datatype == INT) {
|
||||
if (cols == 0) {
|
||||
int *vec = *((int **) pdata);
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
|
||||
} else {
|
||||
int **array = *((int ***) pdata);
|
||||
for (m = 0; m < cols; m++)
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][j++]).i);
|
||||
}
|
||||
} else if (datatype == BIGINT) {
|
||||
if (cols == 0) {
|
||||
bigint *vec = *((bigint **) pdata);
|
||||
fprintf(fp," " BIGINT_FORMAT,(bigint) ubuf(buf[i][j++]).i);
|
||||
} else {
|
||||
bigint **array = *((bigint ***) pdata);
|
||||
for (m = 0; m < cols; m++)
|
||||
fprintf(fp," " BIGINT_FORMAT,(bigint) ubuf(buf[i][j++]).i);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -444,19 +444,6 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
|
|||
if ((universe->me == 0) && !helpflag) {
|
||||
if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version);
|
||||
if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version);
|
||||
#if defined(LAMMPS_CXX98)
|
||||
const char warning[] = "\nWARNING-WARNING-WARNING-WARNING-WARNING\n"
|
||||
"This LAMMPS executable was compiled using C++98 compatibility.\n"
|
||||
"Please report the compiler info below at https://github.com/lammps/lammps/issues/1659\n";
|
||||
const char *infobuf = Info::get_compiler_info();
|
||||
if (screen)
|
||||
fprintf(screen,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n",
|
||||
warning,infobuf);
|
||||
if (logfile)
|
||||
fprintf(logfile,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n",
|
||||
warning,infobuf);
|
||||
delete[] infobuf;
|
||||
#endif
|
||||
}
|
||||
|
||||
// universe is one or more worlds, as setup by partition switch
|
||||
|
|
|
|||
|
|
@ -833,8 +833,16 @@ TEST(PairStyle, intel) {
|
|||
GTEST_SKIP();
|
||||
}
|
||||
|
||||
if (test_config.pair_style == "rebo") {
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
cleanup_lammps(lmp,test_config);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
std::cerr << "Skipping pair style rebo/intel\n";
|
||||
GTEST_SKIP();
|
||||
}
|
||||
|
||||
// relax error a bit for USER-INTEL package
|
||||
double epsilon = 5.0*test_config.epsilon;
|
||||
double epsilon = 7.5*test_config.epsilon;
|
||||
|
||||
// we need to relax the epsilon a LOT for tests using long-range
|
||||
// coulomb with tabulation. seems more like mixed precision or a bug
|
||||
|
|
@ -916,6 +924,11 @@ TEST(PairStyle, intel) {
|
|||
double energy = lmp->modify->compute[id]->compute_scalar();
|
||||
EXPECT_FP_LE_WITH_EPS(pair->eng_vdwl, test_config.run_vdwl, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(pair->eng_coul, test_config.run_coul, epsilon);
|
||||
|
||||
// rebo family of pair styles will have a large error in per-atom energy for USER-INTEL
|
||||
if (test_config.pair_style.find("rebo") != std::string::npos)
|
||||
epsilon *= 100000.0;
|
||||
|
||||
EXPECT_FP_LE_WITH_EPS((pair->eng_vdwl+pair->eng_coul),energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_energy stats:" << stats << std::endl;
|
||||
|
|
|
|||
|
|
@ -0,0 +1,115 @@
|
|||
LAMMPS data file via write_data, version 5 May 2020, timestep = 100
|
||||
|
||||
48 atoms
|
||||
2 atom types
|
||||
|
||||
-2.4861156578082535e+00 8.9861156578082539e+00 xlo xhi
|
||||
-2.4819903352214698e+00 8.9819903352214627e+00 ylo yhi
|
||||
-4.3054203125591495e-02 5.1588542031255695e+00 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01
|
||||
2 1.00794
|
||||
|
||||
Atoms # atomic
|
||||
|
||||
1 1 -2.4341520800875485e-01 -1.7599524940425884e-01 1.7253026363065874e-02 0 0 0
|
||||
2 2 6.2959178506621150e-01 -8.1199640633841275e-01 5.0650728892557169e+00 0 0 -1
|
||||
3 2 -1.1121054450754664e+00 -8.3279707540106163e-01 7.2096452612715661e-02 0 0 0
|
||||
4 1 -7.5984840129235773e-02 5.7591620256483522e-01 1.3343679301805187e+00 0 0 0
|
||||
5 2 8.5789395758423881e-01 1.1360995499761726e+00 1.3392878065261780e+00 0 0 0
|
||||
6 2 -8.9514139407768334e-01 1.2810979866887890e+00 1.4672917222565367e+00 0 0 0
|
||||
7 1 -7.8922730413067493e-02 -4.7479369963754220e-01 2.5185123359600543e+00 0 0 0
|
||||
8 2 6.9190595505201324e-01 -1.2323705910769223e+00 2.4967645244437549e+00 0 0 0
|
||||
9 2 -1.0542989182028326e+00 -8.6670850317437531e-01 2.7742498749957547e+00 0 0 0
|
||||
10 1 -3.9293923764317451e-01 7.9768136737711803e-01 4.0780146018561370e+00 0 0 0
|
||||
11 2 2.6489159244845972e-01 6.3268071552307958e-01 3.1065632452221319e+00 0 0 0
|
||||
12 2 -1.1276632977587033e+00 1.6002955633500584e+00 4.0362106311025991e+00 0 0 0
|
||||
25 1 2.8193998846172103e-01 4.9716388907291211e+00 1.2606338151319968e-01 0 0 0
|
||||
26 2 6.3688650225373622e-01 3.9416691414211957e+00 8.4663335521264788e-02 0 0 0
|
||||
27 2 -2.0208077533780515e+00 2.5949325118859128e+00 5.0202232238943560e+00 0 0 -1
|
||||
28 1 -7.4168338315013638e-01 5.2218024150822453e+00 1.2248307190256451e+00 0 0 0
|
||||
29 2 -4.8179493715117638e-01 6.1236479529318952e+00 1.7794910195025608e+00 0 0 0
|
||||
30 2 -1.7176232502059992e+00 5.3891340038772491e+00 7.6757849370604592e-01 0 0 0
|
||||
31 1 -8.2930357027190393e-01 4.0508256977629209e+00 2.1889173835557001e+00 0 0 0
|
||||
32 2 6.0059642714797988e-02 3.5652543084424897e+00 2.5883670569486474e+00 0 0 0
|
||||
33 2 -1.7771933013123182e+00 3.7284700023378750e+00 2.6194240236976913e+00 0 0 0
|
||||
34 1 7.0934043141810477e-01 5.8634734699961584e+00 4.4708075530959954e+00 0 0 0
|
||||
35 2 1.4298800972607446e+00 5.6733729534659272e+00 3.6739058245879264e+00 0 0 0
|
||||
36 2 3.8569508794682422e-01 6.9038536556618695e+00 4.4511164881858134e+00 0 0 0
|
||||
13 1 5.3833228071964809e+00 -7.9766421392727882e-01 4.9067271264856016e+00 0 0 -1
|
||||
14 2 6.1381564762115239e+00 -7.8202480607143987e-01 4.9424348568586329e-01 0 0 0
|
||||
15 2 4.9519600117886347e+00 -1.7940020475946012e+00 4.8110945764576156e+00 0 0 -1
|
||||
16 1 4.2645777622126220e+00 1.3426567813575572e+00 1.9093414401493067e+00 0 0 0
|
||||
17 2 5.2992823900063506e+00 1.6374691057747635e+00 1.7460953493055651e+00 0 0 0
|
||||
18 2 3.5099850408886284e+00 1.8099079050100266e+00 1.2774250930764246e+00 0 0 0
|
||||
19 1 3.8688841475335543e+00 2.3194408557219204e-01 2.9625536035071800e+00 0 0 0
|
||||
20 2 4.4341357385042519e+00 -7.1331393747926441e-01 2.5617272090593692e+00 0 0 0
|
||||
21 2 2.8376541614717623e+00 -2.2192921113968814e-01 2.5457530111814437e+00 0 0 0
|
||||
22 1 5.0378949110324136e+00 2.3252709541752614e-01 4.1826607654379533e+00 0 0 0
|
||||
23 2 5.4732646659003770e+00 1.2253893824970703e+00 4.3037885157885949e+00 0 0 0
|
||||
24 2 3.2481280364389118e+00 8.2567333665575415e-01 3.7760702420134979e+00 0 0 0
|
||||
37 1 4.1662535153421656e+00 4.5773898294151056e+00 -1.0050993206243145e-02 0 0 0
|
||||
38 2 4.9392137394956936e+00 3.8125893258627546e+00 5.2693482707363397e-02 0 0 0
|
||||
39 2 3.1995812686514005e+00 4.0802938177597321e+00 5.1370804386657056e+00 0 0 -1
|
||||
40 1 4.2110798207275053e+00 5.4794783309775354e+00 1.2640511411782265e+00 0 0 0
|
||||
41 2 5.1714048300399131e+00 5.9965367483183840e+00 1.2752754545998148e+00 0 0 0
|
||||
42 2 3.4278850616533649e+00 6.2349719582368124e+00 1.1809837259994789e+00 0 0 0
|
||||
43 1 4.0344354881156264e+00 4.7341737056781810e+00 2.5920156833691146e+00 0 0 0
|
||||
44 2 5.9018244698732047e+00 2.9062392498170997e+00 2.6599377379111933e+00 0 0 0
|
||||
45 2 3.3647742541156997e+00 3.8770609870643540e+00 2.6263801261664406e+00 0 0 0
|
||||
46 1 4.3864129291324065e+00 5.4385557345189968e+00 3.9068248851528278e+00 0 0 0
|
||||
47 2 5.4322503572891048e+00 5.7470767535646932e+00 3.8793919420623091e+00 0 0 0
|
||||
48 2 3.7782712922559569e+00 6.3393431995123084e+00 3.9888830689083061e+00 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 -1.0894444084053871e+00 1.2179758936956877e+00 1.1079806495668135e-01
|
||||
2 1.6877845887054355e+00 1.3056535723402372e+00 2.6561381291171191e+00
|
||||
3 -3.1125663897940310e+00 1.6529463325047355e+00 -4.0034715419532665e+00
|
||||
4 -1.1557050859943641e+00 -1.1836562561048363e+00 -1.2552320014721685e+00
|
||||
5 3.9983598869475645e+00 1.0340503455549954e+00 2.8100380170215185e+00
|
||||
6 5.1092451702327493e+00 -3.9141586462940986e-01 6.2633396565144273e-01
|
||||
7 1.0307982395927142e+00 -1.2606300928185629e-01 -2.8206938844989836e-02
|
||||
8 -6.1963844586525672e-02 1.5367728661944744e+00 -1.6165066090802973e+00
|
||||
9 5.9246559865739123e-01 1.7618681246069584e-01 -1.7712296302906054e+00
|
||||
10 2.2580329076027261e-02 -1.1064033888047093e+00 -8.4543250413064619e-01
|
||||
11 2.7527292315030985e+00 -8.4549696409899500e-01 -1.6649408346851993e+00
|
||||
12 2.2551594965037169e-01 4.0427187315766098e+00 -4.6646230929080152e+00
|
||||
25 -3.4216979727798102e-01 2.6515660067898694e-01 -4.1153207161407163e-01
|
||||
26 4.8780948317346393e+00 3.3594615440046387e+00 -1.7251088924872291e+00
|
||||
27 3.4230423525981633e+00 5.7326721971736438e-01 4.1159603478846511e+00
|
||||
28 -1.2430127296124194e+00 8.4712600153098727e-01 -1.4444463305442226e-02
|
||||
29 -4.7244436356582273e+00 4.8891316822495341e+00 -2.3254053488248032e+00
|
||||
30 -4.7413901140247372e+00 5.3815030555326331e+00 -1.0828996770519246e+00
|
||||
31 -6.2008075007494567e-01 9.1617269551362390e-01 2.3142026319364109e-01
|
||||
32 4.2266796565992841e+00 2.5453270169936268e+00 -4.8321190043502371e-01
|
||||
33 -4.6135662901311782e+00 -1.9728957639302671e+00 -3.0374188716470223e+00
|
||||
34 4.0114701075701914e-01 1.4151504196514619e-01 1.4817950597700830e-01
|
||||
35 4.1358822022551971e+00 -1.8243773216029848e+00 -7.2472363609030288e-01
|
||||
36 4.6340930144944625e+00 2.4576344600576472e+00 5.0626747539766868e+00
|
||||
13 1.8278069366103494e-01 5.2342341602105624e-01 -6.0423794796060226e-01
|
||||
14 4.9390070605030276e+00 2.1021116363725221e+00 2.0486606910290217e-01
|
||||
15 -4.9993254261382736e-01 -4.6980992366373302e+00 2.8677140594068162e+00
|
||||
16 7.8343591908967891e-01 -3.3780594158195848e-01 1.4671535586247206e+00
|
||||
17 -1.8418238503512363e+00 2.9037305513734619e+00 -4.4823250896128389e-02
|
||||
18 -1.8876740682082613e+00 3.6977793758646254e+00 -7.1976453348094083e-01
|
||||
19 1.1160256125335217e+00 -3.8469582576856409e-01 1.3566081850646794e-01
|
||||
20 -3.5794369426869292e+00 -4.2485734281342564e+00 2.5679481394581951e+00
|
||||
21 4.6400734263468575e+00 -2.7006328994236486e+00 2.5920610885986042e+00
|
||||
22 -5.2238413509963677e-01 -9.9964685063253012e-01 -4.9342929458022622e-01
|
||||
23 -1.8036726500469569e+00 -4.8244704690808271e-01 2.8954691667568189e+00
|
||||
24 3.8243074390853242e+00 2.8226264709240891e+00 -4.5665850315188749e-03
|
||||
37 1.0560596585528772e+00 -1.0741413123517354e+00 -4.6177958544062769e-01
|
||||
38 -4.3048610332410373e+00 -2.0121669185838891e+00 2.6598958497710523e+00
|
||||
39 -3.3591849767473567e+00 -9.6050957527058711e-01 -9.0169345872103590e-01
|
||||
40 1.9193383706614244e-02 1.3336541742820790e-01 9.3466008986781524e-01
|
||||
41 3.4751244640977843e+00 -1.1523945163243521e+00 -2.9448921878292245e+00
|
||||
42 2.7087738982055294e+00 9.4561842351091427e-02 8.1539452331144333e-02
|
||||
43 -4.8968596347171067e-01 5.9091455453317410e-01 1.0488500207673568e+00
|
||||
44 2.6912081704725952e+00 7.4631405042237164e-01 -4.0069184028303733e+00
|
||||
45 1.0744157293309868e+00 -4.6574530734219959e+00 -8.5404163785692366e-01
|
||||
46 -6.2272628902830041e-01 -6.8959866091615207e-01 2.0230104819190772e-01
|
||||
47 -4.9707138179571322e+00 -2.4357921349417890e+00 5.0196115666859775e+00
|
||||
48 -1.9619565986884380e+00 2.1496720750712592e+00 -3.5468158775431577e+00
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
variable newton_pair index on
|
||||
variable newton_bond index on
|
||||
variable units index metal
|
||||
variable input_dir index .
|
||||
variable data_file index ${input_dir}/data.airebo
|
||||
variable pair_style index 'zero 8.0'
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
neigh_modify delay 2 every 2 check no
|
||||
timestep 0.0005
|
||||
units ${units}
|
||||
newton ${newton_pair} ${newton_bond}
|
||||
|
||||
pair_style ${pair_style}
|
||||
read_data ${data_file}
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:13:46 202
|
||||
epsilon: 1e-7
|
||||
prerequisites: ! |
|
||||
pair airebo
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: airebo 3.0 1 1
|
||||
pair_coeff: ! |
|
||||
* * CH.airebo C H
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: -184.951215338583
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
9.0890487540552234e-02 5.6086429553227568e-01 2.1197563114732207e-01 1.4104429996380902e-01 1.4152302642812123e-01 9.2650318538687204e-01
|
||||
init_forces: ! |2
|
||||
1 8.0445098702263997e-03 8.8637342321642477e-03 7.9370914431606456e-03
|
||||
2 7.3942077145426480e-04 -1.5836483503449159e-02 1.4455583179877503e-02
|
||||
3 -1.8733284429445950e-02 3.0633584100819723e-02 -4.8704635212019239e-03
|
||||
4 5.5107808376383179e-03 -9.3517479290550678e-03 5.4116855126747517e-05
|
||||
5 1.7335625961861563e-02 -1.3790958304619322e-02 1.7759552343702956e-02
|
||||
6 -2.0462842106868809e-03 -1.2419421765559397e-02 1.0506397047082559e-02
|
||||
7 -1.5825368937762482e-01 -4.7929841314322691e-01 -2.7555752286490282e-01
|
||||
8 7.2556741066172872e-03 -6.2665679124310524e-03 -1.3275912983560631e-02
|
||||
9 -1.9888402254035150e-02 -2.4174414683628364e-02 -3.3455936336250644e-02
|
||||
10 2.7135056702712605e-02 3.5419388439985759e-02 3.6881290892835900e-02
|
||||
11 5.2786515239602615e-02 4.5232747763254749e-01 2.0143778501318141e-01
|
||||
12 -1.3587311593963690e-02 5.2747472177613443e-03 7.8730106343171277e-02
|
||||
25 -1.4236876677876844e-02 -8.7145855177811534e-03 1.4530082980973478e-02
|
||||
26 -6.9353447717636378e-03 -5.4658022818302411e-03 1.0919180432182594e-02
|
||||
27 2.8680768312074813e-02 -4.2389957664550303e-02 -4.4718283685937998e-02
|
||||
28 1.5505654369865249e-03 2.0311951864006410e-03 -1.3111838688803234e-02
|
||||
29 2.3095293880332123e-02 1.4302833135070145e-02 -5.3918365556458230e-02
|
||||
30 -1.8081699216798707e-02 -1.9212566259036515e-03 3.1153446323732618e-02
|
||||
31 1.4356001380203071e-02 -2.6069899525343415e-04 -4.3953834348586657e-02
|
||||
32 1.7903711503520440e-02 1.7912670869351718e-02 -3.0587054548599956e-02
|
||||
33 1.3917567086515524e-03 2.6393313057161052e-02 -5.2132293141950378e-02
|
||||
34 -3.1771367322591573e-02 1.4793725813198566e-02 4.0350312463455995e-02
|
||||
35 -4.3104368125507213e-02 -3.3015130699775644e-02 6.5548374282321131e-02
|
||||
36 -9.8548912590153710e-03 2.3913427800464713e-02 2.6810099505576258e-02
|
||||
13 -1.2507751483945622e-02 -1.6077922930149865e-02 -4.0766638666415417e-02
|
||||
14 -1.8541175418693236e-02 2.8024212503724114e-02 -5.4408810588732683e-02
|
||||
15 1.4778056088016463e-02 -3.4284884444071559e-02 -2.6926360961490533e-02
|
||||
16 1.1682520558454540e-02 -3.4803375161147959e-03 3.7313458006501619e-02
|
||||
17 1.4492245755486710e-02 -1.3845110766828260e-02 1.6103567776786176e-02
|
||||
18 -7.1763609843851842e-03 -3.0161738206889381e-02 4.9477423111201957e-02
|
||||
19 1.3278263169619262e-02 -2.1923284934318751e-03 9.8503521559582616e-03
|
||||
20 3.6694164712439539e-02 -3.0742875397548356e-03 3.6928879888744472e-02
|
||||
21 1.0532660003247417e-02 -2.8766223079886910e-02 2.7300164664698715e-02
|
||||
22 -1.9759228194633697e-03 2.1833972167343554e-03 -1.9189541028449969e-02
|
||||
23 -6.0033660801034859e-03 4.6415206482854797e-03 -1.2173650358869588e-02
|
||||
24 1.8289297203356290e-02 3.2292794912946468e-02 -3.1779548830552028e-02
|
||||
37 -5.3749623436340540e-03 2.9367809115355761e-03 1.1488795653112617e-04
|
||||
38 3.0850541467722834e-03 -4.0744480202252169e-03 -1.6187312210134541e-02
|
||||
39 -2.0711633525865154e-02 9.9351890468012821e-03 6.1417342933701461e-03
|
||||
40 1.1118517806702732e-02 1.8481525198274576e-03 4.1777838880835427e-04
|
||||
41 3.1170233998653759e-02 -1.5448707079099688e-02 -1.1973868526731797e-02
|
||||
42 3.3575265992803185e-03 4.8849463883252463e-03 1.6770888985230834e-03
|
||||
43 5.5073880031353672e-03 2.8635891324946736e-02 6.2957963487790831e-03
|
||||
44 5.2278697709017604e-03 -5.9205396052392717e-03 -1.1641028263524280e-02
|
||||
45 8.2446804237109976e-03 2.2000009725752060e-02 8.2390814628951456e-07
|
||||
46 -6.4059561000704031e-04 1.5796469864722801e-02 8.7781880557686095e-03
|
||||
47 1.5239882999050557e-02 -3.1268760745643753e-03 1.8994686979097005e-02
|
||||
48 9.4124555469617685e-04 2.8313380234794853e-02 1.4160015571855478e-02
|
||||
run_vdwl: -184.686733268654
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-8.3410051971885424e-01 1.3625323642932721e+00 4.1461501508495013e+00 8.6688227256219996e-01 1.5565717748380517e-01 1.4790555833058188e+00
|
||||
run_forces: ! |2
|
||||
1 -2.7566525107809318e-02 -1.8961404924034975e-01 5.5232231950330789e-03
|
||||
2 -1.2758309231200282e-01 -1.9769482352839155e-02 -6.3019726921142868e-02
|
||||
3 7.6250703896397640e-02 -8.9398464495202608e-03 1.1147884265844542e-01
|
||||
4 2.3085246545061733e-01 3.1284937254363476e-01 -7.3585264863498745e-01
|
||||
5 -1.9144857312851615e-01 -1.2515355098923714e-01 -1.5959719844577522e-01
|
||||
6 -1.9647387066787372e-01 5.8583959861360932e-02 -5.5802890003857034e-02
|
||||
7 -7.4393491306453985e-01 -2.1031898155941424e+00 -1.3179845766973441e+00
|
||||
8 1.4451248841145776e-02 -7.5094603421028893e-03 5.1335942947151741e-03
|
||||
9 6.3511525939309199e-02 2.9090392490561837e-02 1.3303386864174215e-02
|
||||
10 -1.9672634807891523e-01 1.8083728118630801e-01 4.5651093638569429e-01
|
||||
11 8.4872388548445898e-01 1.9358940575890571e+00 1.7628952060030210e+00
|
||||
12 1.5987186106095264e-01 -9.8208391350393887e-02 1.2853301921141560e-02
|
||||
25 -6.4229350400654264e-02 6.5121223305082257e-02 1.0056877607918861e-01
|
||||
26 -1.7220602843542449e-01 -1.1015144383642610e-01 3.6631722097947343e-02
|
||||
27 2.1703726611672525e-02 -3.5813737565299292e-02 -3.8490244907288140e-02
|
||||
28 -7.9119032244579168e-02 1.3730457326547163e-01 -1.8741773388952015e-01
|
||||
29 1.0488978251101254e-01 -1.1909435018113117e-01 3.7305458437005917e-02
|
||||
30 1.5288232489842238e-01 -1.7372783419202745e-01 5.5596050035545151e-02
|
||||
31 2.7049702020580869e-02 8.7269359923485251e-02 -8.0188955708864224e-02
|
||||
32 -1.5669855197695848e-01 2.6784824182432453e-02 -1.4149188090162742e-02
|
||||
33 1.4491176754189819e-01 5.7431352138432642e-03 -3.3994471687721864e-02
|
||||
34 1.4553829964664816e-01 1.6556081633947264e-01 1.3970048432616899e-01
|
||||
35 -1.0616681119412462e-01 4.6690438466217482e-02 7.4629391229118824e-02
|
||||
36 -7.4068565095854799e-02 -8.2089870709701862e-02 -1.3462256268225453e-01
|
||||
13 8.2379101312774386e-02 -3.7742159339381581e-01 7.7965598133185904e-02
|
||||
14 -1.5216836068437717e-01 2.2238518425134669e-02 -6.8256075141941222e-02
|
||||
15 1.3519830621083784e-01 1.8694222750179545e-01 -4.5760020752184015e-02
|
||||
16 -9.4122812277554868e-02 3.7460162964963219e-02 -1.8223514295685489e-01
|
||||
17 6.3613595149790536e-02 -3.9090346770006286e-02 3.5671486224074810e-02
|
||||
18 7.8916322295767963e-02 -1.2892708246196263e-01 1.4769704074590567e-01
|
||||
19 -8.3810673528647555e-03 -8.5441646265745450e-02 5.3647900953469149e-02
|
||||
20 -1.6539114897139909e-01 2.1397130301406403e-01 -1.0949816014942894e-02
|
||||
21 1.3818067438426573e-01 -6.8993959043769607e-02 -2.1299386806295124e-02
|
||||
22 -1.5856475763177083e-03 1.5748026932167003e-01 7.4938732730195579e-02
|
||||
23 3.9340145378663122e-02 -1.4061855355790968e-02 -9.4604853769769570e-02
|
||||
24 -4.0312184075427006e-02 1.5211975019366620e-02 2.0132865843451725e-02
|
||||
37 -5.7540799130195752e-01 5.0058614364608629e-02 1.7327763650198574e-01
|
||||
38 1.3880800864979662e-01 -1.1430713799896731e-02 -9.5273453741880343e-02
|
||||
39 1.3583699403986030e-01 7.1359222213997292e-02 3.6415542956628806e-02
|
||||
40 2.4826377557322687e-01 -8.7545078947765323e-02 -1.6810450734482277e-01
|
||||
41 -9.9940408667160155e-02 -4.7990932334050156e-02 9.9884783379563344e-02
|
||||
42 -5.1291223401165813e-02 4.7496283547191202e-02 -9.4577003424099033e-04
|
||||
43 3.2988332629179412e-02 -1.0775544344105276e-01 -1.4421909297187224e-01
|
||||
44 7.4156020575267502e-03 -1.6440936142548804e-03 -6.8207536960046720e-03
|
||||
45 6.0379992226191302e-02 1.2659562736103339e-01 2.3394684516017537e-02
|
||||
46 -9.9942524249085951e-02 1.1237800722245612e-01 1.0203699454103866e-01
|
||||
47 1.9442848972770918e-01 6.9497639530798572e-02 -1.3132256701126685e-01
|
||||
48 7.8378396725857863e-02 -1.1885470662272486e-01 1.3371799785827665e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:28:51 202
|
||||
epsilon: 1e-07
|
||||
prerequisites: ! |
|
||||
pair airebo
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: airebo 3.0 0 0
|
||||
pair_coeff: ! |
|
||||
* * CH.airebo C H
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: -184.961290756177
|
||||
init_coul: 0
|
||||
init_stress: ! |-
|
||||
-1.5991107880755417e-02 1.7140062289608402e+00 -1.0794915656416637e+00 4.8928377143354418e-01 1.4299757801250498e-01 9.1729270327881118e-01
|
||||
init_forces: ! |2
|
||||
1 1.3152583785902394e-01 4.8753765297722407e-02 -1.5563723988713196e-01
|
||||
2 -6.4677574125421855e-02 -3.6433365193474787e-02 -1.3515634466513748e-01
|
||||
3 1.6366540055346573e-03 1.6053102235330685e-02 -1.4025763253580847e-02
|
||||
4 -8.7465878593573243e-02 -4.5665446908147445e-02 6.9471852842624970e-02
|
||||
5 1.3196006750610195e-02 -8.8650251156534021e-03 4.7800865230702150e-02
|
||||
6 1.9299301808352459e-02 3.2589957088717370e-02 9.4282242729599730e-02
|
||||
7 -3.4087548212679419e-01 -1.2294752667452695e+00 -5.1904944997164693e-01
|
||||
8 6.0078617802455783e-02 2.0498628992936883e-02 -9.3398597244978704e-03
|
||||
9 1.2467192886648326e-02 3.8099500610843495e-02 1.4081370285705760e-01
|
||||
10 -1.2918644768262050e-01 -2.1668533156799785e-02 -1.3804629901508914e-01
|
||||
11 3.2262037268716748e-01 1.1759176707599115e+00 5.8980717273254846e-01
|
||||
12 1.4376037289299093e-02 6.2603438310488174e-02 8.4228698980900824e-02
|
||||
27 4.7005361439318077e-02 -5.2408426176605377e-02 -5.5149578856349829e-02
|
||||
21 -5.0710356947559279e-02 -1.4285676294952748e-01 -3.0103912730198391e-02
|
||||
24 7.8265517181488331e-03 4.3251923864515054e-02 -5.8933854751528125e-02
|
||||
13 -3.5716712652627103e-02 1.3735681410832867e-02 1.4393711826134470e-02
|
||||
14 -2.7941716820501609e-02 3.1552257494521507e-02 -4.2877340897456456e-02
|
||||
15 1.5196317529582337e-02 -2.4839376668334828e-02 -5.3559475071731644e-02
|
||||
16 7.3420523773577977e-03 3.7613136334306359e-02 -2.8703713987937803e-02
|
||||
17 1.5584476459449964e-02 9.8879114554081271e-03 5.0428356540854230e-02
|
||||
18 -1.1905338802559173e-04 6.3435717951509374e-03 3.8589803704210474e-02
|
||||
19 -3.6317481447328021e-02 1.5667256621317516e-01 5.7218527576755107e-02
|
||||
20 4.5103361944769826e-02 -5.6143964618761297e-02 1.1055811359300005e-01
|
||||
22 2.1264619496304038e-02 -5.8783062697015775e-02 5.6556265461199795e-03
|
||||
23 4.1238140118919062e-02 -9.3062149465309579e-03 -5.7265617948053335e-02
|
||||
44 -2.7501983884904435e-03 -7.1276666877394812e-03 -5.4002244001689348e-03
|
||||
25 -9.4094738859907934e-02 7.9609978294326034e-04 -7.8044314532108583e-02
|
||||
26 4.4149651971254422e-02 1.1780662578757373e-02 5.7158432441624774e-02
|
||||
28 3.4569663809708134e-02 -2.0908322434320625e-01 -2.7708578780154147e-02
|
||||
29 5.2910800566559682e-04 6.4293440655586787e-02 -9.5734647942841478e-02
|
||||
30 -2.5656282692781196e-02 8.9866518259576811e-02 7.6113053684404353e-02
|
||||
31 3.4736314391823564e-02 1.0807969068365202e-01 1.4868993579665887e-01
|
||||
32 1.7988755611627966e-02 -3.0751094993370962e-02 -8.7482941885915211e-02
|
||||
33 -9.3425588225226341e-03 -2.1584491055374688e-02 -9.3877008553606200e-02
|
||||
34 -1.5684631199890900e-02 1.5044628958073569e-03 1.4853366946912826e-02
|
||||
35 3.1768878922333800e-02 -3.8885849858596389e-02 5.5946517738598732e-02
|
||||
36 -1.8964161137310365e-02 2.3983785394224535e-02 3.0086185086425243e-02
|
||||
39 -1.9729521703836572e-02 -6.3932341883306376e-02 -3.2518573786006422e-02
|
||||
37 -1.3157059382780328e-01 1.5168014676918418e-01 4.1142179440578630e-04
|
||||
38 -1.5988753846897796e-03 -2.5960455382179282e-02 2.0267750800645690e-02
|
||||
40 1.6488495970003630e-01 -2.1535919097797926e-01 -3.0400741445342494e-02
|
||||
41 -2.3107048489258319e-02 9.3912679031607021e-02 7.4598236747208668e-03
|
||||
42 5.2864856296723328e-02 4.7976966093041584e-02 -5.4878418640677884e-02
|
||||
43 -3.4984194842396499e-01 2.7616124926611707e-01 3.3585356232387786e-02
|
||||
45 1.8178724152826475e-01 -1.8028798863029671e-01 -3.3398498292016243e-02
|
||||
46 7.6023397517703095e-02 -2.2544487533539470e-01 4.2072193193403246e-02
|
||||
47 -7.6877574240748030e-04 5.5783708545097566e-02 -2.0995954025529923e-02
|
||||
48 5.1056308529232042e-02 8.5470102504109025e-02 6.8395640494008869e-02
|
||||
run_vdwl: -185.084340567887
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-1.3323153386673774e+00 6.5009894327154760e-02 -1.7326291586383442e+00 4.9671868735735564e-01 2.8136179703319608e-02 5.7806981457586715e-01
|
||||
run_forces: ! |2
|
||||
1 6.8355528493844298e-02 -1.1944451443270802e-01 -4.4125204825235098e-01
|
||||
2 -1.2861924608968991e-01 -4.4137097431923344e-02 -1.2751824466012474e-01
|
||||
3 8.1494435661480014e-02 -3.6920590518428054e-03 1.0040642950505263e-01
|
||||
4 3.7527017608456914e-01 6.6940856681461991e-02 5.8019895967875557e-01
|
||||
5 -1.8393789675484831e-01 -1.5834568564675960e-01 -8.6224034419114470e-02
|
||||
6 -1.7282212455395130e-01 4.5083734857249647e-02 3.1197253351678889e-02
|
||||
7 -3.3619376905194437e-01 -5.8091977753188084e-01 -5.8107276386347717e-01
|
||||
8 1.0273233422549642e-01 -8.5412334130676976e-02 5.6323287362551079e-02
|
||||
9 -1.3215510856196822e-02 -3.8099218776399491e-02 2.0437541579240195e-01
|
||||
10 1.6412187218573659e-01 4.5430627507431653e-01 -7.0297693657988702e-01
|
||||
11 -4.9902630586834862e-02 6.7017696686888217e-01 8.2705477529688232e-01
|
||||
12 5.2147711171131816e-02 -1.6146646227932876e-01 1.8929213157343128e-01
|
||||
27 4.0569120071207609e-02 -4.4990684200391068e-02 -4.9804224785798434e-02
|
||||
21 1.6856210984353245e-01 -7.9511292426074076e-02 1.0001675896785096e-02
|
||||
24 -9.2732980601280657e-02 -1.0950138658861922e-02 -4.0836736654732086e-02
|
||||
13 6.4751997045543686e-02 -3.5563305441624971e-01 1.2820269624458880e-01
|
||||
14 -1.5333471357819128e-01 1.5914151143699928e-02 -6.5037280503974712e-02
|
||||
15 1.2286738982966094e-01 1.9265004204325895e-01 -4.9637041122573833e-02
|
||||
16 -1.0852990429909931e-01 7.3201982309721483e-02 -2.4712787611616815e-01
|
||||
17 6.0229575881071917e-02 -1.8934283782071015e-02 6.7629621559359809e-02
|
||||
18 9.6466429473633097e-02 -9.9301800509148969e-02 1.5137717899747341e-01
|
||||
19 -7.7003389183944088e-02 -2.3023763423969890e-02 4.8266701905256490e-02
|
||||
20 -1.7916905871455191e-01 1.9867797610853855e-01 4.8402207345646708e-02
|
||||
22 3.4304140788237750e-02 1.3519423218540497e-01 6.6300981648753990e-02
|
||||
23 6.2839752037413682e-02 -2.6370577409609117e-02 -1.1545103162740503e-01
|
||||
44 7.4865147797376075e-04 -1.9134731646395786e-03 -2.0910975730097647e-03
|
||||
25 -1.2036034340714141e-01 5.2468101598679873e-02 4.3362109026140239e-02
|
||||
26 -1.3709346740420025e-01 -9.5632079961340877e-02 5.9007750969542250e-02
|
||||
28 -6.4018377994091560e-02 6.0553928500104437e-02 -1.8776358251620712e-01
|
||||
29 9.6890302093696382e-02 -1.2338057085228121e-01 6.7295979231108971e-03
|
||||
30 1.5163669686192729e-01 -1.4218642480904720e-01 7.9473882014891972e-02
|
||||
31 3.1597012409922437e-02 1.8162006569087685e-01 8.0853434851491893e-02
|
||||
32 -1.5574245261504957e-01 -1.4903833490853655e-02 -5.9160677478346482e-02
|
||||
33 1.4736721012005907e-01 -3.2985065985107143e-02 -6.7005897560507538e-02
|
||||
34 2.2444726480772675e-01 1.4487810359056891e-01 7.1462055528190113e-02
|
||||
35 -8.5673030495807490e-02 6.1015455839103921e-02 1.2177185351699812e-01
|
||||
36 -8.9050814377041709e-02 -9.1447680120703895e-02 -1.4873052627530475e-01
|
||||
39 1.5210289064479374e-01 6.3318639778475738e-02 2.3309631651053708e-02
|
||||
37 -6.2333640474717122e-01 5.1087346671760403e-02 1.7873483824820902e-01
|
||||
38 1.1822724805114426e-01 1.3806051076594161e-03 -7.8201063267624660e-02
|
||||
40 2.9670421707793115e-01 -1.4891122500091292e-01 -2.2577727039126999e-01
|
||||
41 -1.1163722101360789e-01 -1.6291547452462640e-02 1.1570402265470292e-01
|
||||
42 -2.8439534417055767e-02 4.1199861152822509e-02 -2.5621427173460498e-02
|
||||
43 -3.1571378405888584e-01 3.7002322228513365e-02 -1.2890733821154285e-01
|
||||
45 2.7239277705401937e-01 7.6632675253599444e-03 -9.6378796865211891e-03
|
||||
46 -7.4845763922132422e-02 2.0438477364830343e-02 1.4619059575391516e-01
|
||||
47 1.9442828039042842e-01 7.3643646110724048e-02 -1.5176869728387757e-01
|
||||
48 1.2011729494053558e-01 -1.3053139348677081e-01 1.5597458770641501e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:26:25 202
|
||||
epsilon: 1e-07
|
||||
prerequisites: ! |
|
||||
pair airebo/morse
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: airebo/morse 3.0 1 1
|
||||
pair_coeff: ! |
|
||||
* * CH.airebo-m C H
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: -184.906791169779
|
||||
init_coul: 0
|
||||
init_stress: ! |-
|
||||
-1.9905840837585734e-01 9.9992116160260081e-01 -8.7107008837839661e-01 3.8867690764878343e-01 1.6780936142412156e-01 1.2045504927890958e+00
|
||||
init_forces: ! |2
|
||||
1 -2.0517729766528860e-02 -1.4262995534169765e-02 -7.7963887627594861e-02
|
||||
2 -2.3292944549651143e-02 -6.7249828039017299e-03 -7.6793499917455169e-02
|
||||
3 -1.4092849573913088e-02 3.1805962926497053e-02 -3.4138357265727254e-02
|
||||
4 2.1899004604710474e-03 -4.1989704976489765e-03 6.0201335634925482e-03
|
||||
5 2.0241700654822448e-02 -1.5556027189412708e-02 2.6728671619349303e-02
|
||||
6 1.1456048207589772e-02 4.4358273015205740e-03 9.1675791034385529e-02
|
||||
7 -3.4229132775085536e-01 -1.1972452864837069e+00 -5.5203863487263571e-01
|
||||
8 5.6656469172808935e-02 2.2263235858918210e-02 -2.8744416882031344e-03
|
||||
9 7.0652957250645796e-03 1.2292922029980341e-03 6.8027547762351426e-02
|
||||
10 1.6474826872584381e-02 5.1697228896774222e-02 -4.6429635472860976e-02
|
||||
11 2.7359825402660776e-01 1.1591131630022211e+00 5.7604317521182036e-01
|
||||
12 -1.6966183404425326e-02 2.0005776678633208e-02 7.4285303443834383e-02
|
||||
25 -1.0348914179117446e-02 -1.5363032067927010e-02 3.8497206556342453e-03
|
||||
26 3.6217728899200518e-03 -5.9579941688302062e-03 1.8307533288494764e-02
|
||||
27 3.9412960252465476e-02 -5.4780576877686678e-02 -5.3261154604627423e-02
|
||||
28 2.0208534504483162e-03 2.1660794039467311e-03 -1.0074165724085796e-02
|
||||
29 3.1523279098070039e-02 1.3231992100660369e-02 -4.1037220112554042e-02
|
||||
30 -1.7935081092400468e-02 -2.2567940364334811e-03 3.0924622213973543e-02
|
||||
31 2.4301072874938292e-02 -2.0260797985721227e-02 -2.9066138023701869e-02
|
||||
32 2.1291997787850396e-02 2.0049030065209292e-02 -2.8173565609265250e-02
|
||||
33 3.8103121956027056e-03 2.0953495479834640e-02 -5.0688470245415417e-02
|
||||
34 -3.5368448227485742e-02 4.0323812525656016e-04 1.2036955050128079e-02
|
||||
35 2.1975636221484500e-03 -3.4548771183920565e-02 6.1836819899349076e-02
|
||||
36 -1.0160663159000431e-02 2.3509241970262711e-02 2.8066559971084468e-02
|
||||
13 -2.0459845454245021e-02 -4.1468146718981668e-03 -1.9151815940882014e-02
|
||||
14 -2.3418059180109290e-02 3.0544955460059132e-02 -4.9090761147108801e-02
|
||||
15 1.1656783637493524e-02 -2.8358346908418989e-02 -4.0123034264605187e-02
|
||||
16 1.2765577695696089e-02 2.6181592218778943e-02 1.3256906225680189e-02
|
||||
17 1.5271823911694370e-02 -1.9104098352645177e-02 1.4787739004554422e-02
|
||||
18 -9.5060935539167460e-03 1.9643783746141224e-03 5.6998482114197217e-02
|
||||
19 1.4229646387889518e-02 -3.5381316056916153e-03 7.7461982718596972e-03
|
||||
20 4.5404064978554808e-02 -9.7586517126307219e-03 3.8251778495346195e-02
|
||||
21 -6.3057799134156184e-02 -5.1054562301407494e-02 2.3619313205612120e-02
|
||||
22 -6.2315350167798204e-03 1.1745903233472599e-02 2.8902034055890333e-03
|
||||
23 -9.7471817248659821e-03 8.6921151015094036e-03 -1.1241037752092215e-02
|
||||
24 1.8650178962035604e-02 3.2818240007903177e-02 -3.1102047239755275e-02
|
||||
37 -8.7435994030670393e-03 3.1191405936012743e-04 1.7887396320730308e-03
|
||||
38 2.5273964519169851e-03 -1.1504733773486877e-02 -1.3157241144539459e-02
|
||||
39 -4.0646716094586713e-02 6.4275738930320136e-03 -5.4473387074653688e-03
|
||||
40 1.0568584242762576e-02 1.9565157477192006e-03 -2.0095242662941738e-04
|
||||
41 3.2440796644272754e-02 -1.6908051806037914e-02 -1.3019233412209725e-02
|
||||
42 9.0435754174252661e-03 6.5794830651171431e-03 -3.6354784764202321e-02
|
||||
43 -4.9001503636347888e-03 2.6746242116619755e-02 9.4368754420029784e-03
|
||||
44 4.8308252882241862e-03 -5.8630425989018757e-03 -1.0391993922486365e-02
|
||||
45 1.9202706435960823e-02 -3.5826931807379711e-02 -1.1278558300301649e-02
|
||||
46 -1.2686955525069661e-02 1.5757428775066942e-02 7.5875168576671499e-03
|
||||
47 1.3552850486712849e-02 -1.4399850633487542e-03 1.9372348907855261e-02
|
||||
48 -3.5635040678223824e-02 1.8069673365221146e-02 4.9559034910065504e-02
|
||||
run_vdwl: -184.884287638713
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-1.7553297389663807e+00 -2.0601635049893026e+00 -1.2914715105335668e+00 -1.2164852300255997e-01 -4.6612665537491982e-01 -1.7584106513907777e-01
|
||||
run_forces: ! |2
|
||||
1 -4.7056658298582076e-04 -1.4634222942799394e-01 -3.1706476526805027e-01
|
||||
2 -1.3535142579879833e-01 -3.4314289056189752e-02 -1.0367582735591681e-01
|
||||
3 6.8650003463217715e-02 -8.3697069795512120e-03 9.6833809476059018e-02
|
||||
4 4.2071591222775861e-01 1.7283632620651795e-01 3.9136383645688072e-01
|
||||
5 -1.7865994780460992e-01 -1.4611726831783364e-01 -1.1398589448509859e-01
|
||||
6 -1.7784101851934428e-01 4.5618526085822425e-02 1.8657271970413374e-02
|
||||
7 2.3090519777513271e-01 9.6499512779086294e-01 3.5569275071901496e-01
|
||||
8 6.8680141620648019e-02 -6.5043644160050693e-02 3.3101755591902426e-02
|
||||
9 1.4039981406452870e-02 -5.8844391944973380e-02 9.9688858750920539e-02
|
||||
10 5.3646218762077855e-02 4.9904730056839725e-01 -2.3006541661968963e-01
|
||||
11 -4.4688380209968831e-01 -1.0148824359301210e+00 -3.2575486748268678e-01
|
||||
12 5.9125769005741756e-02 -1.6455074843131096e-01 1.4182565053188184e-01
|
||||
25 -5.8830023005069586e-02 5.5493152701298960e-02 8.9356007987085137e-02
|
||||
26 -1.6126938215990105e-01 -1.0589550989698598e-01 4.4457820280718992e-02
|
||||
27 3.2050225113605772e-02 -4.6858682187267103e-02 -4.6030115729389323e-02
|
||||
28 -7.5947731462843282e-02 1.3782694351300281e-01 -1.7799302352415669e-01
|
||||
29 1.0756252212717538e-01 -1.2493903809259364e-01 3.7463632651968878e-02
|
||||
30 1.5346237725582387e-01 -1.7193789085169181e-01 5.7093382017703226e-02
|
||||
31 3.7100886471736753e-02 6.6328162647684819e-02 -6.8241776528602388e-02
|
||||
32 -1.5386863547969926e-01 3.1563293915620398e-02 -1.1714437764915764e-02
|
||||
33 1.4713421544405372e-01 2.1760039530633707e-04 -3.2616373504918299e-02
|
||||
34 1.9064328958682114e-01 1.4591501668099530e-01 9.8409456596864342e-02
|
||||
35 -9.9846542261889978e-02 5.2704676893072323e-02 9.6991422347650041e-02
|
||||
36 -7.6502955446541621e-02 -8.5095668829058016e-02 -1.3897135591211321e-01
|
||||
13 7.4818684100851671e-02 -3.6120445920708949e-01 9.3359386334273653e-02
|
||||
14 -1.5618766168829912e-01 2.0408313847255815e-02 -6.3657252717194857e-02
|
||||
15 1.3274432075484421e-01 1.8890222305075144e-01 -5.3774497785697782e-02
|
||||
16 -1.0939749808088689e-01 7.0297915308787498e-02 -2.0655632465075238e-01
|
||||
17 6.6926827327773053e-02 -4.4104673887093666e-02 3.3117350168894881e-02
|
||||
18 8.4614454722492821e-02 -1.0145181052862164e-01 1.6550368839223134e-01
|
||||
19 -4.1619642190982541e-02 -9.6396190853089911e-02 4.1403847715373324e-02
|
||||
20 -1.9839035226178811e-01 2.1599992066411777e-01 -1.3457232824090459e-02
|
||||
21 1.5383852967224548e-01 -7.2701207696353312e-02 -5.0818378502930973e-04
|
||||
22 -9.4230270862067055e-03 1.7342238753231365e-01 9.0815029821744414e-02
|
||||
23 3.4558368487069897e-02 -1.2078171184596179e-02 -9.1321557338724546e-02
|
||||
24 -4.7349089756643828e-02 7.0930724599967106e-03 9.2840611032212628e-03
|
||||
37 -5.9216580817461095e-01 1.2321315564060400e-02 1.7075406198563545e-01
|
||||
38 1.3228377510993414e-01 -1.4179759288390884e-02 -9.3273292141222208e-02
|
||||
39 1.4106998279682412e-01 7.9136335255856782e-02 3.3231256275553296e-02
|
||||
40 2.4863765861074733e-01 -8.9429039881233977e-02 -1.8767583738581864e-01
|
||||
41 -9.8668584541866278e-02 -5.0568392084021939e-02 9.8367911149062015e-02
|
||||
42 -4.9260030547804493e-02 4.8085923600047889e-02 -1.2364163270556597e-02
|
||||
43 -1.1397987292289991e-02 -1.4101799789272826e-01 -1.4770764058051941e-01
|
||||
44 6.9144141741118775e-03 -2.2619416778199885e-03 -6.2863438078055783e-03
|
||||
45 1.0662201618495948e-01 1.1264787973634517e-01 1.1636487874690335e-02
|
||||
46 -1.4095023595362419e-01 1.1420276586190301e-01 1.2027784751424971e-01
|
||||
47 1.8817799678511232e-01 7.9435207983366785e-02 -1.2950610265865653e-01
|
||||
48 6.5358179209163397e-02 -1.3591423997672408e-01 1.4351569940761391e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:29:04 202
|
||||
epsilon: 1e-07
|
||||
prerequisites: ! |
|
||||
pair airebo/morse
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: airebo/morse 3.0 0 0
|
||||
pair_coeff: ! |
|
||||
* * CH.airebo-m C H
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: -184.961290756177
|
||||
init_coul: 0
|
||||
init_stress: ! |-
|
||||
-1.5991107880755417e-02 1.7140062289608402e+00 -1.0794915656416637e+00 4.8928377143354418e-01 1.4299757801250498e-01 9.1729270327881118e-01
|
||||
init_forces: ! |2
|
||||
1 1.3152583785902394e-01 4.8753765297722407e-02 -1.5563723988713196e-01
|
||||
2 -6.4677574125421855e-02 -3.6433365193474787e-02 -1.3515634466513748e-01
|
||||
3 1.6366540055346573e-03 1.6053102235330685e-02 -1.4025763253580847e-02
|
||||
4 -8.7465878593573243e-02 -4.5665446908147445e-02 6.9471852842624970e-02
|
||||
5 1.3196006750610195e-02 -8.8650251156534021e-03 4.7800865230702150e-02
|
||||
6 1.9299301808352459e-02 3.2589957088717370e-02 9.4282242729599730e-02
|
||||
7 -3.4087548212679419e-01 -1.2294752667452695e+00 -5.1904944997164693e-01
|
||||
8 6.0078617802455783e-02 2.0498628992936883e-02 -9.3398597244978704e-03
|
||||
9 1.2467192886648326e-02 3.8099500610843495e-02 1.4081370285705760e-01
|
||||
10 -1.2918644768262050e-01 -2.1668533156799785e-02 -1.3804629901508914e-01
|
||||
11 3.2262037268716748e-01 1.1759176707599115e+00 5.8980717273254846e-01
|
||||
12 1.4376037289299093e-02 6.2603438310488174e-02 8.4228698980900824e-02
|
||||
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|
||||
21 -5.0710356947559279e-02 -1.4285676294952748e-01 -3.0103912730198391e-02
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
47 -7.6877574240748030e-04 5.5783708545097566e-02 -2.0995954025529923e-02
|
||||
48 5.1056308529232042e-02 8.5470102504109025e-02 6.8395640494008869e-02
|
||||
run_vdwl: -185.084340567887
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-1.3323153386673774e+00 6.5009894327154760e-02 -1.7326291586383442e+00 4.9671868735735564e-01 2.8136179703319608e-02 5.7806981457586715e-01
|
||||
run_forces: ! |2
|
||||
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|
||||
2 -1.2861924608968991e-01 -4.4137097431923344e-02 -1.2751824466012474e-01
|
||||
3 8.1494435661480014e-02 -3.6920590518428054e-03 1.0040642950505263e-01
|
||||
4 3.7527017608456914e-01 6.6940856681461991e-02 5.8019895967875557e-01
|
||||
5 -1.8393789675484831e-01 -1.5834568564675960e-01 -8.6224034419114470e-02
|
||||
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|
||||
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|
||||
8 1.0273233422549642e-01 -8.5412334130676976e-02 5.6323287362551079e-02
|
||||
9 -1.3215510856196822e-02 -3.8099218776399491e-02 2.0437541579240195e-01
|
||||
10 1.6412187218573659e-01 4.5430627507431653e-01 -7.0297693657988702e-01
|
||||
11 -4.9902630586834862e-02 6.7017696686888217e-01 8.2705477529688232e-01
|
||||
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|
||||
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|
||||
21 1.6856210984353245e-01 -7.9511292426074076e-02 1.0001675896785096e-02
|
||||
24 -9.2732980601280657e-02 -1.0950138658861922e-02 -4.0836736654732086e-02
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
26 -1.3709346740420025e-01 -9.5632079961340877e-02 5.9007750969542250e-02
|
||||
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|
||||
29 9.6890302093696382e-02 -1.2338057085228121e-01 6.7295979231108971e-03
|
||||
30 1.5163669686192729e-01 -1.4218642480904720e-01 7.9473882014891972e-02
|
||||
31 3.1597012409922437e-02 1.8162006569087685e-01 8.0853434851491893e-02
|
||||
32 -1.5574245261504957e-01 -1.4903833490853655e-02 -5.9160677478346482e-02
|
||||
33 1.4736721012005907e-01 -3.2985065985107143e-02 -6.7005897560507538e-02
|
||||
34 2.2444726480772675e-01 1.4487810359056891e-01 7.1462055528190113e-02
|
||||
35 -8.5673030495807490e-02 6.1015455839103921e-02 1.2177185351699812e-01
|
||||
36 -8.9050814377041709e-02 -9.1447680120703895e-02 -1.4873052627530475e-01
|
||||
39 1.5210289064479374e-01 6.3318639778475738e-02 2.3309631651053708e-02
|
||||
37 -6.2333640474717122e-01 5.1087346671760403e-02 1.7873483824820902e-01
|
||||
38 1.1822724805114426e-01 1.3806051076594161e-03 -7.8201063267624660e-02
|
||||
40 2.9670421707793115e-01 -1.4891122500091292e-01 -2.2577727039126999e-01
|
||||
41 -1.1163722101360789e-01 -1.6291547452462640e-02 1.1570402265470292e-01
|
||||
42 -2.8439534417055767e-02 4.1199861152822509e-02 -2.5621427173460498e-02
|
||||
43 -3.1571378405888584e-01 3.7002322228513365e-02 -1.2890733821154285e-01
|
||||
45 2.7239277705401937e-01 7.6632675253599444e-03 -9.6378796865211891e-03
|
||||
46 -7.4845763922132422e-02 2.0438477364830343e-02 1.4619059575391516e-01
|
||||
47 1.9442828039042842e-01 7.3643646110724048e-02 -1.5176869728387757e-01
|
||||
48 1.2011729494053558e-01 -1.3053139348677081e-01 1.5597458770641501e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:29:21 202
|
||||
epsilon: 1e-07
|
||||
prerequisites: ! |
|
||||
pair rebo
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! ""
|
||||
input_file: in.airebo
|
||||
pair_style: rebo
|
||||
pair_coeff: ! |
|
||||
* * CH.rebo C H
|
||||
extract: ! ""
|
||||
natoms: 48
|
||||
init_vdwl: -184.39204996406
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
3.3789835306128507e-01 2.9478711461049310e+00 2.4743519134193620e-01 5.2979459234337423e-01 5.3569422394689620e-02 -6.3505274336891904e-03
|
||||
init_forces: ! |2
|
||||
1 1.4202190879785526e-01 -1.6923984230378553e-02 -8.0222747253743343e-02
|
||||
2 -6.4677585143091409e-02 -3.6433357195058524e-02 -1.3515634272432853e-01
|
||||
3 1.6366649982768461e-03 1.6053110519967689e-02 -1.4025763949495174e-02
|
||||
4 -8.7465877246782064e-02 -4.5665431983584470e-02 6.9471854481199857e-02
|
||||
5 1.3195994863209298e-02 -8.8650322236522028e-03 4.7800865172213158e-02
|
||||
6 1.9299312240111804e-02 3.2589948135326341e-02 9.4282241042096482e-02
|
||||
7 -3.4087548299692300e-01 -1.2294752754679814e+00 -5.1904944459948887e-01
|
||||
8 6.0078607638260430e-02 2.0498638968231599e-02 -9.3398594218969955e-03
|
||||
9 1.2467205701909068e-02 3.8099505743407369e-02 1.4081369951564779e-01
|
||||
10 -1.4036212729933867e-01 4.9553606683401752e-02 -2.1963701282202114e-01
|
||||
11 3.2484928214165820e-01 1.1715484924862587e+00 5.9205862013599853e-01
|
||||
12 4.5455440111838996e-03 7.0650496984066086e-02 9.7280898658545945e-02
|
||||
27 5.5286552293670688e-02 -6.1630718420004310e-02 -6.4277008234728178e-02
|
||||
21 -4.7676041551031507e-02 -1.4184636978150536e-01 -2.8031242280102477e-02
|
||||
24 7.1293499799228721e-03 4.1506393546603043e-02 -6.0982020307679297e-02
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
23 4.5058119107672233e-02 -1.1595478876420868e-02 -5.2231218382529837e-02
|
||||
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|
||||
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|
||||
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|
||||
28 -6.5526188863108709e-02 -1.0387188938520331e-01 2.2724432063331967e-02
|
||||
29 5.2910469917024153e-04 6.4293429254679846e-02 -9.5734654968105404e-02
|
||||
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|
||||
31 2.8687599814099147e-02 2.7435698043211158e-02 2.1404025944551910e-01
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
36 -2.4762906521939687e-02 2.2322971056000673e-02 3.7646653163387167e-02
|
||||
39 -1.9729509365073616e-02 -6.3932335561141695e-02 -3.2518573086913416e-02
|
||||
37 -1.3157059618544575e-01 1.5168013170222649e-01 4.1142188933296353e-04
|
||||
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|
||||
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|
||||
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|
||||
42 5.2864866169949176e-02 4.7976956598500820e-02 -5.4878417596658124e-02
|
||||
43 -3.9860425909811842e-01 1.2112577926727722e-01 3.4047365974571434e-02
|
||||
45 1.7935918713998519e-01 -1.7837444575824185e-01 -3.2987232446594350e-02
|
||||
46 1.0998928173472683e-01 -1.5086188432942196e-01 1.6829691363685131e-01
|
||||
47 -7.6878894879590064e-04 5.5783704671116340e-02 -2.0995953677601979e-02
|
||||
48 5.1056316250091771e-02 8.5470091106617740e-02 6.8395639456075963e-02
|
||||
run_vdwl: -184.51998480396
|
||||
run_coul: 0
|
||||
run_stress: ! |-
|
||||
-9.7239038536264044e-01 7.4669322717364839e-01 -7.7104364903424294e-01 5.4771494015343014e-01 -2.1796905704783737e-02 1.5820274570202170e-01
|
||||
run_forces: ! |2
|
||||
1 7.4155582187185320e-02 -1.5455609952472066e-01 -4.0185659582818589e-01
|
||||
2 -1.2599664371163707e-01 -4.7270532243529007e-02 -1.2614563997376005e-01
|
||||
3 7.9410728544291417e-02 -6.7788695692031498e-03 1.0261863017785233e-01
|
||||
4 3.7589897293458219e-01 6.5448581597716937e-02 5.8478513706716928e-01
|
||||
5 -1.8406250774366176e-01 -1.5832209948748655e-01 -8.6604265862793073e-02
|
||||
6 -1.7291110116223143e-01 4.4906356654481727e-02 3.0419307237807502e-02
|
||||
7 -3.3201513523500364e-01 -5.7108644658989294e-01 -5.7184715922428109e-01
|
||||
8 1.0238297541360618e-01 -8.5807437101430781e-02 5.5823992026930724e-02
|
||||
9 -1.3228565520703811e-02 -3.7950591025267766e-02 2.0421517542414661e-01
|
||||
10 1.4592100832953753e-01 5.0467945019617289e-01 -7.4626980273333943e-01
|
||||
11 -5.1925532167434674e-02 6.6189711468983248e-01 8.1768796712217684e-01
|
||||
12 5.1995519711525773e-02 -1.5927701231286884e-01 1.9862297055802863e-01
|
||||
27 5.0374698419944214e-02 -5.5882415283804526e-02 -6.1449715991752973e-02
|
||||
21 1.6055010729342936e-01 -8.1367480026234451e-02 4.7738041806187972e-03
|
||||
24 -1.0140395868207885e-01 -1.0454584382977056e-02 -4.3414162729483508e-02
|
||||
13 1.1052397822448223e-01 -4.8902847823072948e-01 2.2436653549186952e-01
|
||||
14 -1.2659521957922421e-01 1.2816580952653644e-02 -3.9238318659560040e-02
|
||||
15 1.0828096163587569e-01 1.5750742059927378e-01 -4.9031658140836099e-02
|
||||
16 -9.3819071598751372e-02 1.1363099411041987e-01 -2.8917292131028305e-01
|
||||
17 6.1264072128814004e-02 -1.0300523555956453e-02 7.5263991898455590e-02
|
||||
18 9.3662574156401057e-02 -9.7235276408278087e-02 1.4807349757758884e-01
|
||||
19 -1.3885588032919249e-01 -5.8043962338309218e-02 2.8993245656022994e-02
|
||||
20 -1.7941687952715857e-01 1.9675979738168892e-01 4.8524391854859461e-02
|
||||
22 2.9757987689549029e-02 2.6821741595825943e-01 5.0099879446351969e-03
|
||||
23 8.0001033580391123e-02 9.3334873087038556e-03 -1.0495490808234802e-01
|
||||
44 -3.9497049925369954e-03 -1.1835391368516579e-02 -9.1934856815404364e-03
|
||||
25 -1.0758122712185991e-01 -7.4031425832087994e-02 7.9729207343358754e-02
|
||||
26 -1.1995670080895027e-01 -1.3389321888390909e-01 5.7892521051779777e-02
|
||||
28 -1.4765203681698147e-01 1.0766945779400883e-01 -1.2725063867138145e-01
|
||||
29 9.8604349817134632e-02 -1.1569372528116473e-01 1.0229831981692472e-02
|
||||
30 1.4286353986949066e-01 -1.3879111821390899e-01 7.8927078553209795e-02
|
||||
31 1.3924003711072844e-02 1.3544044195264066e-01 1.3574982086169629e-01
|
||||
32 -1.5074384592659218e-01 -1.6814340709227951e-02 -5.7556964094494831e-02
|
||||
33 1.4184429434188114e-01 -3.5285331907102369e-02 -6.4237440338038271e-02
|
||||
34 2.8579134215307045e-01 2.6727531865785603e-01 -5.8543384904504128e-02
|
||||
35 -6.1822738170098798e-02 5.8781336914225123e-02 9.2908986409371730e-02
|
||||
36 -9.5270981048167308e-02 -5.4657394491328407e-02 -1.4784901819268981e-01
|
||||
39 1.5246274787180031e-01 6.3970465119924325e-02 2.2789344570593340e-02
|
||||
37 -6.2050313799109447e-01 6.2522082639067444e-02 1.7931449902055974e-01
|
||||
38 1.1783097105703605e-01 1.6630970573315029e-03 -7.7576019986230649e-02
|
||||
40 3.0652623048947314e-01 -1.0727327421957705e-01 -3.0878707410990303e-01
|
||||
41 -1.0805211258372868e-01 -1.2213265101714554e-02 1.1407035371979291e-01
|
||||
42 -3.0772480548032222e-02 4.6330303739023915e-02 -2.8690841675368839e-02
|
||||
43 -3.4159822655899680e-01 -6.1488889554779033e-02 -1.2996240931199338e-01
|
||||
45 2.5974287224213982e-01 -5.1237846099988077e-03 -9.2705797475414742e-03
|
||||
46 -5.2983750718683130e-02 6.0115740314057198e-02 2.2945318498880257e-01
|
||||
47 1.9907355212167138e-01 7.7186684778662140e-02 -1.4956254800833946e-01
|
||||
48 1.1827333461841494e-01 -1.2568916016199683e-01 1.5822209053962674e-01
|
||||
...
|
||||
|
|
@ -25,34 +25,50 @@ protected:
|
|||
const char *args[] = {"PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite" };
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args)/sizeof(char *);
|
||||
::testing::internal::CaptureStdout();
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
|
||||
void TearDown() override {
|
||||
::testing::internal::CaptureStdout();
|
||||
delete lmp;
|
||||
::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
};
|
||||
|
||||
TEST_F(PotenialFileReaderTest, Si) {
|
||||
::testing::internal::CaptureStdout();
|
||||
PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairSW::Param::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairSW::Param::NPARAMS_PER_LINE);
|
||||
}
|
||||
|
||||
TEST_F(PotenialFileReaderTest, Comb) {
|
||||
::testing::internal::CaptureStdout();
|
||||
PotentialFileReader reader(lmp, "ffield.comb", "COMB");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairComb::Param::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairComb::Param::NPARAMS_PER_LINE);
|
||||
}
|
||||
|
||||
TEST_F(PotenialFileReaderTest, Comb3) {
|
||||
::testing::internal::CaptureStdout();
|
||||
PotentialFileReader reader(lmp, "ffield.comb3", "COMB3");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairComb3::Param::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairComb3::Param::NPARAMS_PER_LINE);
|
||||
}
|
||||
|
||||
TEST_F(PotenialFileReaderTest, Tersoff) {
|
||||
::testing::internal::CaptureStdout();
|
||||
PotentialFileReader reader(lmp, "Si.tersoff", "Tersoff");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairTersoff::Param::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairTersoff::Param::NPARAMS_PER_LINE);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue