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python interface for per-atom data for fix external

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This commit is contained in:
Axel Kohlmeyer
2021-07-22 15:27:51 -04:00
parent bb46dd7d1f
commit 324ae3181b
3 changed files with 109 additions and 4 deletions
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52
python/lammps/core.py
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@ -1749,8 +1749,8 @@ class lammps(object):
- ntimestep is the current timestep
- nlocal is the number of local atoms on the current MPI process
- tag is a 1d NumPy array of integers representing the atom IDs of the local atoms
- x is a 2d NumPy array of floating point numbers of the coordinates of the local atoms
- f is a 2d NumPy array of floating point numbers of the forces on the local atoms that will be added
- x is a 2d NumPy array of doubles of the coordinates of the local atoms
- f is a 2d NumPy array of doubles of the forces on the local atoms that will be added
:param fix_id: Fix-ID of a fix external instance
:type: string
@ -1777,7 +1777,7 @@ class lammps(object):
# -------------------------------------------------------------------------
def fix_external_get_force(self, fix_id):
"""Get access to that array with per-atom forces of a fix external instance with a given fix ID.
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
of the C-library interface.
@ -1827,6 +1827,52 @@ class lammps(object):
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_virial_global(self.lmp, fix_id.encode(), cvirial)
# -------------------------------------------------------------------------
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the global energy contribution for a fix external instance with the given ID.
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: list of potential energy values for local atoms to be added by fix external
:type: float
"""
nlocal = self.extract_setting('nlocal')
ceatom = (nlocal*c_double)(*eatom)
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_energy_peratom(self.lmp, fix_id.encode(), ceatom)
# -------------------------------------------------------------------------
def fix_external_set_virial_peratom(self, fix_id, virial):
"""Set the global virial contribution for a fix external instance with the given ID.
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
of the C-library interface.
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: list of natoms lists with 6 floating point numbers to be added by fix external
:type: float
"""
# copy virial data to C compatible buffer
nlocal = self.extract_setting('nlocal')
vbuf = (c_double * 6)
vptr = POINTER(c_double)
cvirial = (vptr * nlocal)()
for i in range(nlocal):
cvirial[i] = vbuf()
for j in range(6):
cvirial[i][j] = virial[i][j]
with ExceptionCheck(self):
return self.lib.lammps_fix_external_set_virial_peratom(self.lmp, fix_id.encode(), cvirial)
# -------------------------------------------------------------------------
def fix_external_set_vector_length(self, fix_id, length):
"""Set the vector length for a global vector stored with fix external for analysis