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implement setting per-atom virial from numpy array (thanks to stackoverflow)

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This commit is contained in:
Axel Kohlmeyer
2021-07-22 22:50:05 -04:00
parent a078d1ba53
commit c8cc5ecb9f
2 changed files with 41 additions and 18 deletions
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16
python/lammps/numpy_wrapper.py
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@ -17,7 +17,7 @@
################################################################################
import warnings
from ctypes import POINTER, c_double, c_int, c_int32, c_int64, cast
from ctypes import POINTER, c_void_p, c_char_p, c_double, c_int, c_int32, c_int64, cast
from .constants import * # lgtm [py/polluting-import]
@ -301,10 +301,6 @@ class numpy_wrapper:
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. note::
This function is not yet implemented.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy
@ -317,6 +313,16 @@ class numpy_wrapper:
if len(vatom[0]) != 6:
raise Exception('per-atom virial second dimension must be 6')
c_double_pp = np.ctypeslib.ndpointer(dtype=np.uintp, ndim=1, flags='C')
# recast numpy array to be compatible with library interface
value = (vatom.__array_interface__['data'][0]
+ np.arange(vatom.shape[0])*vatom.strides[0]).astype(np.uintp)
# change prototype to our custom type
self.lmp.lib.lammps_fix_external_set_virial_peratom.argtypes = [ c_void_p, c_char_p, c_double_pp ]
self.lmp.lib.lammps_fix_external_set_virial_peratom(self.lmp.lmp, fix_id.encode(), value)
# -------------------------------------------------------------------------