def addColvars(self, name, cvType, atomIDs):
"""
Implements the addition of a collective variable to the list of collective variables held by this walker.
Arguments:
-----------------------
name -
A internal string used to reference this collective variable. Collective variable names must be unique.
cvType -
A string refering to the type of collective variable. Currently the following variables are supported:
* 'bond'
* 'angle'
* 'dihedral'
* 'x', 'y', 'z' positions
* 'x', 'y', 'z' velocity components
atomIDs -
A list of the atom indecies involved in the collective variable. Should provide the right number of atom indecies for the collective variable:
* 'bond' -> 2
* 'angle'-> 3
* 'dihedral' -> 4
* position or velocity component -> 1
"""
# make sure we know what the cv type is.
__knownCVs__ = ['x', 'y', 'z', 'vx', 'vy', 'vz']
assert cvType in __knownCVs__, "cvType that was provided was not understood."
# check to make sure the name is unique.
for cv in self.colvars:
assert cv.name != name, "Collective variable names must be unique."
# now append the collective variable to the walker list. Initialize a collective variable object.
self.colvars.append(collectiveVariables.collectiveVariables(name, cvType, atomIDs))
return 0
def add_colvars(self, name, cvType, atomIDs):
"""
Implements the addition of a collective variable to the list of collective variables held by this walker.
Arguments:
-----------------------
name -
A internal string used to reference this collective variable. Collective variable names must be unique.
cvType -
A string refering to the type of collective variable. Currently the following variables are supported:
* 'bond'
* 'angle'
* 'dihedral'
* 'x', 'y', 'z' positions
* 'x', 'y', 'z' velocity components
atomIDs -
A list of the atom indecies involved in the collective variable. Should provide the right number of atom indecies for the collective variable:
* 'bond' -> 2
* 'angle'-> 3
* 'dihedral' -> 4
* position or velocity component -> 1
"""
# make sure we know what the cv type is.
__knownCVs__ = ['bond', 'angle', 'dihedral', 'x', 'y', 'z', 'vx', 'vy', 'vz', 'fe']
assert cvType in __knownCVs__, "cvType that was provided was not understood."
# check to make sure the name is unique.
for cv in self.colvars:
assert cv.name != name, "Collective variable names must be unique."
# now append the collective variable to the walker list. Initialize a collective variable object.
self.colvars.append(collectiveVariables.collectiveVariables(name, cvType, atomIDs))
# grab a handle to the new object
cv = self.colvars[-1]
# first set the group for the colvar
self.command("group " + cv.name + " id " + " ".join(map(str,cv.atomIDs)))
# now set the appropriate colvar as a compute to LAMMPS
if cv.type == 'bond':
self.command("compute " + cv.name + " " + cv.name + " bond/local dist" )
elif cv.type == 'angle':
self.command("compute " + cv.name + " " + cv.name + " angle/local theta")
elif cv.type == 'dihedral':
self.command("compute " + cv.name + " " + cv.name + " dihedral/local phi")
elif cv.type == 'x':
self.command("compute " + cv.name + " " + cv.name + " property/atom x")
elif cv.type == 'y':
self.command("compute " + cv.name + " " + cv.name + " property/atom y")
elif cv.type == 'z':
self.command("compute " + cv.name + " " + cv.name + " property/atom z")
elif cv.type == "vx":
self.command("compute " + cv.name + " " + cv.name + " property/atom vx")
elif cv.type == "vy":
self.command("compute " + cv.name + " " + cv.name + " property/atom vy")
elif cv.type == "vz":
self.command("compute " + cv.name + " " + cv.name + " property/atom vz")
self.propagate(0, pre='yes')
self.ref_cv = self.get_colvars()
return 0
