def reset(self):
"""
Reset data members to default values.
"""
self.myForceFields = list()
self.energies = Energies()
self.forces.fill(0)
def reset(self):
"""
Reset data members to default values.
"""
self.myForceFields = list()
self.energies = Energies()
self.forces.fill(0)
def __init__(self):
#####################################################################
# USER-ACCESSIBLE STRUCTURES
self.myForceFields = list() #: Array of MDL force fields
self.energies = Energies() #: Holds system energies
# NOTE: self.forces is a numpy array which holds system forces.
#####################################################################
#########################################################
# NOTE: USER SHOULD NOT TOUCH THIS!
# THIS IS A WRAPPER FOR THE FORCE ARRAY
# WHICH IS ACCESSIBLE THROUGH self.force
self.__dict__['forcevec'] = Vector3DBlock.Vector3DBlock()
#self.force = 0 #: Atomic force vector.
#########################################################
self.accept = 0
self.reject = 0
def __init__(self):
#####################################################################
# USER-ACCESSIBLE STRUCTURES
self.myForceFields = list() #: Array of MDL force fields
self.energies = Energies() #: Holds system energies
# NOTE: self.forces is a numpy array which holds system forces.
#####################################################################
#########################################################
# NOTE: USER SHOULD NOT TOUCH THIS!
# THIS IS A WRAPPER FOR THE FORCE ARRAY
# WHICH IS ACCESSIBLE THROUGH self.force
self.__dict__['forcevec'] = Vector3DBlock.Vector3DBlock()
#self.force = 0 #: Atomic force vector.
#########################################################
self.accept = 0
self.reject = 0
class Forces:
"""
Contains the atomic force vector, and a structure
to hold system energies.
"""
def __init__(self):
#####################################################################
# USER-ACCESSIBLE STRUCTURES
self.myForceFields = list() #: Array of MDL force fields
self.energies = Energies() #: Holds system energies
# NOTE: self.forces is a numpy array which holds system forces.
#####################################################################
#########################################################
# NOTE: USER SHOULD NOT TOUCH THIS!
# THIS IS A WRAPPER FOR THE FORCE ARRAY
# WHICH IS ACCESSIBLE THROUGH self.force
self.__dict__['forcevec'] = Vector3DBlock.Vector3DBlock()
#self.force = 0 #: Atomic force vector.
#########################################################
self.accept = 0
self.reject = 0
# SPECIAL ACCESSOR FOR self.forces
# TO GET DATA FROM WRAPPERS
def __getattr__(self, name):
if (name == 'force'):
return self.__dict__['forcevec'].getC()
else:
return self.__dict__[name]
# SPECIAL ASSIGNMENT FOR self.forces
# TO SET DATA IN WRAPPERS
def __setattr__(self, name, val):
if (name == 'force' and self.__dict__.has_key('force')):
self.__dict__['forcevec'].setC(val)
else:
self.__dict__[name] = val
def __str__(self):
return "Forces.Forces"
def __repr__(self):
return "Forces.Forces"
def initializeEnergies(self, app):
"""
Initialize the energies structure.
"""
self.energies = app.energies
# RESET SYSTEM STATE TO DEFAULTS
def reset(self):
"""
Reset data members to default values.
"""
self.myForceFields = list()
self.energies = Energies()
self.forces.fill(0)
# CREATE A FORCE FIELD AND APPEND IT TO THE END
# OF THE ARRAY.
# ALSO RETURN THE NEW FORCE FIELD POINTER.
def makeForceField(self, phys, *args):
"""
Create a new MDL force field.
@type phys: Physical
@param phys: The physical system.
@type args: tuple
@param args: Python tuple, may have no values or a string \"charmm\"
@rtype: ForceField
@return: Newly instantiated MDL force field.
"""
ff = ForceField()
ff.charmm = 0
ff.forceFactory = ForceFactory()
if (args.__len__() > 0):
ff.charmm = 1
ff.theforces = self
self.phys = ff.phys = phys
ff.bc = phys.bc
ff.setDefaults()
self.energies.initialize(phys)
ff.thisown = 0
#self.myForceFields.append(ff)
return ff
#return self.myForceFields[self.myForceFields.__len__()-1]
# NOTE: THIS WILL PERMANENTLY DELETE THE PASSED FORCE FIELD OBJECT
# FROM THE ARRAY! USE WITH CAUTION.
def removeForceField(self, ff):
"""
Remove the passed force field from the member list.
@type ff: ForceField
@param ff: MDL force field.
"""
for i in range(0, self.myForceFields.__len__()):
if (self.myForceFields[i] == ff):
self.myForceFields.remove(ff)
break
def randomForce(self, phys, seed):
"""
Compute a random (x, y, z) force.
@type phys: Physical
@param phys: The physical system.
@type seed: integer
@param seed: Random number generator seed.
@rtype: numpy.ndarray
@return: The random force as a three-element array (x,y,z)
"""
retval = numpy.ndarray(phys.numAtoms()*3)
#tmp = numpy.ndarray(3)
ff = 0
while (ff < phys.numAtoms()*3):
retval[ff] = MathUtilities.randomGaussianNumber(seed)
retval[ff+1] = MathUtilities.randomGaussianNumber(seed)
retval[ff+2] = MathUtilities.randomGaussianNumber(seed)
ff += 3
return retval
class Forces:
"""
Contains the atomic force vector, and a structure
to hold system energies.
"""
def __init__(self):
#####################################################################
# USER-ACCESSIBLE STRUCTURES
self.myForceFields = list() #: Array of MDL force fields
self.energies = Energies() #: Holds system energies
# NOTE: self.forces is a numpy array which holds system forces.
#####################################################################
#########################################################
# NOTE: USER SHOULD NOT TOUCH THIS!
# THIS IS A WRAPPER FOR THE FORCE ARRAY
# WHICH IS ACCESSIBLE THROUGH self.force
self.__dict__['forcevec'] = Vector3DBlock.Vector3DBlock()
#self.force = 0 #: Atomic force vector.
#########################################################
self.accept = 0
self.reject = 0
# SPECIAL ACCESSOR FOR self.forces
# TO GET DATA FROM WRAPPERS
def __getattr__(self, name):
if (name == 'force'):
return self.__dict__['forcevec'].getC()
else:
return self.__dict__[name]
# SPECIAL ASSIGNMENT FOR self.forces
# TO SET DATA IN WRAPPERS
def __setattr__(self, name, val):
if (name == 'force' and self.__dict__.has_key('force')):
self.__dict__['forcevec'].setC(val)
else:
self.__dict__[name] = val
def __str__(self):
return "Forces.Forces"
def __repr__(self):
return "Forces.Forces"
def initializeEnergies(self, app):
"""
Initialize the energies structure.
"""
self.energies = app.energies
# RESET SYSTEM STATE TO DEFAULTS
def reset(self):
"""
Reset data members to default values.
"""
self.myForceFields = list()
self.energies = Energies()
self.forces.fill(0)
# CREATE A FORCE FIELD AND APPEND IT TO THE END
# OF THE ARRAY.
# ALSO RETURN THE NEW FORCE FIELD POINTER.
def makeForceField(self, phys, *args):
"""
Create a new MDL force field.
@type phys: Physical
@param phys: The physical system.
@type args: tuple
@param args: Python tuple, may have no values or a string \"charmm\"
@rtype: ForceField
@return: Newly instantiated MDL force field.
"""
ff = ForceField()
ff.charmm = 0
ff.forceFactory = ForceFactory()
if (args.__len__() > 0):
ff.charmm = 1
ff.theforces = self
self.phys = ff.phys = phys
ff.bc = phys.bc
ff.setDefaults()
self.energies.initialize(phys)
ff.thisown = 0
#self.myForceFields.append(ff)
return ff
#return self.myForceFields[self.myForceFields.__len__()-1]
# NOTE: THIS WILL PERMANENTLY DELETE THE PASSED FORCE FIELD OBJECT
# FROM THE ARRAY! USE WITH CAUTION.
def removeForceField(self, ff):
"""
Remove the passed force field from the member list.
@type ff: ForceField
@param ff: MDL force field.
"""
for i in range(0, self.myForceFields.__len__()):
if (self.myForceFields[i] == ff):
self.myForceFields.remove(ff)
break
def randomForce(self, phys, seed):
"""
Compute a random (x, y, z) force.
@type phys: Physical
@param phys: The physical system.
@type seed: integer
@param seed: Random number generator seed.
@rtype: numpy.ndarray
@return: The random force as a three-element array (x,y,z)
"""
retval = numpy.ndarray(phys.numAtoms() * 3)
#tmp = numpy.ndarray(3)
ff = 0
while (ff < phys.numAtoms() * 3):
retval[ff] = MathUtilities.randomGaussianNumber(seed)
retval[ff + 1] = MathUtilities.randomGaussianNumber(seed)
retval[ff + 2] = MathUtilities.randomGaussianNumber(seed)
ff += 3
return retval
#!/usr/bin/python
from sympy import *
from pylab import *
import matplotlib.pyplot as plt
import PairingHamiltonian as ph
import Energies
from WhoKnowsWhat import *
import PairingBasisGenerated as pb
#print dog
correlation_energy_mbpt2 = Energies.corr_mbpt2()
correlation_energy_mbpt3 = Energies.corr_mbpt3()
ga = linspace(-1, 1, 20)
e1 = []
corr2 = []
corr3 = []
for g_val in ga:
H1 = matrix(
[[2 - g_val, -g_val / 2., -g_val / 2., -g_val / 2., -g_val / 2., 0],
[-g_val / 2., 4 - g_val, -g_val / 2., -g_val / 2., 0., -g_val / 2.],
[-g_val / 2., -g_val / 2., 6 - g_val, 0, -g_val / 2., -g_val / 2.],
[-g_val / 2., -g_val / 2., 0, 6 - g_val, -g_val / 2., -g_val / 2.],
[-g_val / 2., 0, -g_val / 2., -g_val / 2., 8 - g_val, -g_val / 2.],
[0, -g_val / 2., -g_val / 2., -g_val / 2., -g_val / 2., 10 - g_val]])
u1, v1 = linalg.eig(H1)
