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add python interface with optional numpy support for lammps_gather_bonds()

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unit tests are included
This commit is contained in:
Axel Kohlmeyer
2021-07-26 22:36:00 -04:00
parent cc87e7eee3
commit 458253b452
9 changed files with 447 additions and 2 deletions
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src/library.cpp
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@ -2695,15 +2695,17 @@ the calling code. The buffer will be filled with bond type, bond atom 1,
bond atom 2 for each bond. Thus the buffer has to be allocated to the
dimension of 3 times the **total** number of bonds times the size of
the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
whether they are stored in 32-bit or 64-bit integers, respectively.
whether they are stored in 32-bit or 64-bit integers, respectively.
This size depends on the compile time settings used when compiling
the LAMMPS library and can be queried by calling
:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
When running in parallel, the data buffer must be allocated on **all**
MPI ranks and will be filled with the information for **all** bonds
in the system.
.. versionadded:: 28Jul2021
Below is a brief C code demonstrating accessing this collected bond information.
.. code-block:: c