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Use modernized LAMMPS Python interface instead of output parsing for Atom properties

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This commit is contained in:
Richard Berger
2021-09-10 12:36:24 -04:00
parent 2627e404b0
commit 41da32d7de
1 changed files with 112 additions and 41 deletions
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153
python/lammps/pylammps.py
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@ -134,6 +134,12 @@ class Atom(object):
def __dir__(self):
return [k for k in super().__dir__() if not k.startswith('_')]
def get(self, name, index):
prop = self._pylmp.lmp.numpy.extract_atom(name)
if prop is not None:
return prop[index]
return None
@property
def id(self):
"""
@ -141,7 +147,7 @@ class Atom(object):
:type: int
"""
return int(self._pylmp.eval("id[%d]" % self.index))
return self.get("id", self.index)
@property
def type(self):
@ -150,7 +156,7 @@ class Atom(object):
:type: int
"""
return int(self._pylmp.eval("type[%d]" % self.index))
return self.get("type", self.index)
@property
def mol(self):
@ -159,7 +165,7 @@ class Atom(object):
:type: int
"""
return self._pylmp.eval("mol[%d]" % self.index)
return self.get("mol", self.index)
@property
def mass(self):
@ -168,52 +174,114 @@ class Atom(object):
:type: float
"""
return self._pylmp.eval("mass[%d]" % self.index)
return self.get("mass", self.index)
@property
def radius(self):
"""
Return the particle radius
:type: float
"""
return self.get("radius", self.index)
@property
def position(self):
"""
:getter: Return position of atom
:setter: Set position of atom
:type: tuple (float, float, float)
:type: numpy.array (float, float, float)
"""
return (self._pylmp.eval("x[%d]" % self.index),
self._pylmp.eval("y[%d]" % self.index),
self._pylmp.eval("z[%d]" % self.index))
return self.get("x", self.index)
@position.setter
def position(self, value):
"""
:getter: Return velocity of atom
:setter: Set velocity of atom
:type: tuple (float, float, float)
"""
self._pylmp.set("atom", self.index, "x", value[0])
self._pylmp.set("atom", self.index, "y", value[1])
self._pylmp.set("atom", self.index, "z", value[2])
current = self.position
current[:] = value
@property
def velocity(self):
return (self._pylmp.eval("vx[%d]" % self.index),
self._pylmp.eval("vy[%d]" % self.index),
self._pylmp.eval("vz[%d]" % self.index))
"""
:getter: Return velocity of atom
:setter: Set velocity of atom
:type: numpy.array (float, float, float)
"""
return self.get("v", self.index)
@velocity.setter
def velocity(self, value):
self._pylmp.set("atom", self.index, "vx", value[0])
self._pylmp.set("atom", self.index, "vy", value[1])
self._pylmp.set("atom", self.index, "vz", value[2])
current = self.velocity
current[:] = value
@property
def force(self):
"""
Return the total force acting on the atom
:type: tuple (float, float, float)
:type: numpy.array (float, float, float)
"""
return (self._pylmp.eval("fx[%d]" % self.index),
self._pylmp.eval("fy[%d]" % self.index),
self._pylmp.eval("fz[%d]" % self.index))
return self.get("f", self.index)
@force.setter
def force(self, value):
current = self.force
current[:] = value
@property
def torque(self):
"""
Return the total torque acting on the atom
:type: numpy.array (float, float, float)
"""
return self.get("torque", self.index)
@force.setter
def torque(self, value):
current = self.torque
current[:] = value
@property
def omega(self):
"""
Return the rotational velocity of the particle
:type: numpy.array (float, float, float)
"""
return self.get("torque", self.index)
@omega.setter
def omega(self, value):
current = self.torque
current[:] = value
@property
def torque(self):
"""
Return the total torque acting on the particle
:type: numpy.array (float, float, float)
"""
return self.get("torque", self.index)
@torque.setter
def torque(self, value):
current = self.torque
current[:] = value
@property
def angular_momentum(self):
"""
Return the angular momentum of the particle
:type: numpy.array (float, float, float)
"""
return self.get("angmom", self.index)
@angular_momentum.setter
def angular_momentum(self, value):
current = self.angular_momentum
current[:] = value
@property
def charge(self):
@ -222,7 +290,7 @@ class Atom(object):
:type: float
"""
return self._pylmp.eval("q[%d]" % self.index)
return self.get("q", self.index)
# -------------------------------------------------------------------------
@ -244,39 +312,42 @@ class Atom2D(Atom):
:getter: Return position of atom
:setter: Set position of atom
:type: tuple (float, float)
:type: numpy.array (float, float)
"""
return (self._pylmp.eval("x[%d]" % self.index),
self._pylmp.eval("y[%d]" % self.index))
return super(Atom2D, self).position[0:2]
@position.setter
def position(self, value):
self._pylmp.set("atom", self.index, "x", value[0])
self._pylmp.set("atom", self.index, "y", value[1])
current = self.position
current[:] = value
@property
def velocity(self):
"""Access to velocity of an atom
:getter: Return velocity of atom
:setter: Set velocity of atom
:type: tuple (float, float)
:type: numpy.array (float, float)
"""
return (self._pylmp.eval("vx[%d]" % self.index),
self._pylmp.eval("vy[%d]" % self.index))
return super(Atom2D, self).velocity[0:2]
@velocity.setter
def velocity(self, value):
self._pylmp.set("atom", self.index, "vx", value[0])
self._pylmp.set("atom", self.index, "vy", value[1])
current = self.velocity
current[:] = value
@property
def force(self):
"""Access to force of an atom
:type: tuple (float, float)
:getter: Return force of atom
:setter: Set force of atom
:type: numpy.array (float, float)
"""
return (self._pylmp.eval("fx[%d]" % self.index),
self._pylmp.eval("fy[%d]" % self.index))
return super(Atom2D, self).force[0:2]
@force.setter
def force(self, value):
current = self.force
current[:] = value
# -------------------------------------------------------------------------