def main():
"""
This test shows how reorder (compress) global IDs for a StructureContainer
"""
p1 = Particle([0.2, 1.3, 33.0], "Si", 2.0, 1.23)
p2 = Particle([5.0, 2.3, -22.1], "C", 1.0, 2.34)
p3 = Particle([5.0, 2.3, -20.1], "C", 1.0, 2.34)
b1 = Bond(1, 2, 1.233, "hooke")
b2 = Bond(2, 3, 0.500, "hooke")
atoms1 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
bonds1 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
polymer1 = StructureContainer(atoms1, bonds1) # Complete structure 1
p1other = Particle([0.0, 2.3, -20.1], "C", 1.0, 2.34)
p2other = Particle([50.0, 0.3, -0.1], "Ar", 2.0, 2.34)
p3other = Particle([50.0, 0.3, -0.1], "Ar", 2.0, 2.34)
b1other = Bond(1, 3, 1.233,
"hooke") # Correct ptclIDs for second structure
atoms2 = ParticleContainer()
atoms2.put(p1other)
atoms2.put(p2other)
atoms2.put(p3other)
del atoms2[2] # remove 2nd particle so ID's are non-consecutive
bonds2 = BondContainer()
bonds2.put(b1other)
polymer2 = StructureContainer(atoms2,
bonds2) # Complete structure 1 completely
del p1, p2, p3, p1other, p2other, b1, b2, b1other, atoms1, atoms2, bonds1, bonds2
print "\n Cleaning memory for initial objects \n"
print "-------------------- Before adding --------------------"
print "polymer1 = ", polymer1
print "polymer2 = ", polymer2
print " "
print "-------------------- After adding --------------------"
polymer2 += polymer1
print "polymer2 = ", polymer2
polymer2.compressPtclIDs()
print "-------------------- After compressing --------------------"
print "polymer2 = ", polymer2
def runStrucAdd(numPtcls1, numPtcls2):
"""
Creates structures with ptcls and bonds between consecutive IDs
Adds and reports timing
Args:
numPtcls1 (int): # of ptcls in first struc
numPtcls2 (int): # of ptcls in second struc
Returns:
(initTime, addTime, compressTime)
"""
atoms1 = ParticleContainer()
bonds1 = BondContainer()
atoms2 = ParticleContainer()
bonds2 = BondContainer()
start_time = time.time()
for n in range(numPtcls1):
pobj1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, float(n + 1))
atoms1.put(pobj1)
for n in range(1, numPtcls1):
bobj1 = Bond(n, n + 1, 1.233, "hooke-1")
bonds1.put(bobj1)
for n in range(numPtcls2):
pobj2 = Particle([2.2, 2.2, 2.2], "C", 1.0, float(n + 1))
atoms2.put(pobj2)
for n in range(1, numPtcls2):
bobj2 = Bond(n, n + 1, 1.233, "hooke-2")
bonds2.put(bobj2)
end_time = time.time()
initTime = end_time - start_time
polymer1 = StructureContainer(atoms1, bonds1) # Complete structure 1
polymer2 = StructureContainer(atoms2, bonds2) # Complete structure 2
del atoms1, atoms2
print "\n Cleaning memory for initial objects \n"
start_time = time.time()
polymer1 += polymer2
end_time = time.time()
addTime = end_time - start_time
start_time = time.time()
polymer1.compressPtclIDs()
end_time = time.time()
compressTime = end_time - start_time
return (numPtcls1, numPtcls2, initTime, addTime, compressTime)
def main():
"""
This test shows compressing IDs when structureContainer has angles included
"""
p1 = Particle([1.1, 1.1, 1.1], "Si", 2.0, 1.23)
p2 = Particle([2.2, 2.2, 2.2], "Si", 1.0, 2.34)
p3 = Particle([3.3, 3.3, 3.3], "Si", 1.0, 2.34)
p4 = Particle([0.0, 0.0, 0.0], "Si", 1.0, 2.34)
#
p5 = Particle([4.4, 4.4, 4.4], "C", 1.0, 2.34) # 1
p6 = Particle([5.5, 5.5, 5.5], "C", 1.0, 2.34) # 2
p7 = Particle([6.6, 6.6, 6.6], "C", 1.0, 2.34) # 3
b1 = Bond(1, 3, 1.11, "hooke")
b2 = Bond(3, 4, 2.22, "hooke")
#
b3 = Bond(1, 2, 3.33, "hooke")
b4 = Bond(2, 3, 4.44, "hooke")
a1 = Angle(1, 3, 4, 1.11, "harmonic")
#
a2 = Angle(1, 2, 3, 2.22, "harmonic")
atoms1 = ParticleContainer()
atoms2 = ParticleContainer()
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
atoms1.put(p4)
#
atoms2.put(p5)
atoms2.put(p6)
atoms2.put(p7)
del atoms1[2] # remove 2nd particle so ID's are non-consecutive
bonds1 = BondContainer()
bonds2 = BondContainer()
bonds1.put(b1)
bonds1.put(b2)
bonds2.put(b3)
bonds2.put(b4)
angles1 = AngleContainer()
angles2 = AngleContainer()
angles1.put(a1)
angles2.put(a2)
polymer1 = StructureContainer(atoms1, bonds1, angles1)
polymer2 = StructureContainer(atoms2, bonds2, angles2)
del p1, p2, p3, p4, p5, p6, b1, b2, b3, b4, a1, a2
del atoms1, atoms2, bonds1, bonds2, angles1, angles2
print "\n Cleaning memory for initial objects \n"
print "-------------------- Initial structures --------------------"
print "polymer1 = ", polymer1
print "polymer2 = ", polymer2
print " "
print "-------------- After adding (polymer2 += polymer1) ----------------"
polymer2 += polymer1
print "polymer2 = ", polymer2
polymer2.compressPtclIDs()
print "-------------------- After compressing --------------------"
print "polymer2 = ", polymer2
def main():
"""
This shows operations on empty StructureContainer objects for 'robustness'
"""
print "************************************************************************************"
print " This shows operations on empty StructureContainer objects for 'robustness'"
print "************************************************************************************ \n"
atoms1 = ParticleContainer()
bonds1 = BondContainer()
p1 = Particle([0.2, 1.3, 33.0], "Si", 2.0, 1.23)
p2 = Particle([5.0, 2.3, -22.1], "C", 1.0, 2.34)
p3 = Particle([5.0, 2.3, -20.1], "C", 1.0, 2.34)
b1 = Bond(1, 2, 1.233, "hooke")
b2 = Bond(2, 3, 0.500, "hooke")
atoms1.put(p1)
atoms1.put(p2)
atoms1.put(p3)
bonds1.put(b1)
bonds1.put(b2)
atoms2 = ParticleContainer()
bonds2 = BondContainer()
polymer1 = StructureContainer(atoms1, bonds1) # Non-empty structure 1
polymer2 = StructureContainer(atoms2, bonds2) # Empty structure 2
# ------------------------------------------------------------------------------------------------------------------------
print "Non-empty container", polymer1
print "Empty container", polymer2
print "Testing empty dump"
polymer2.dump("empty")
print "Testing empty compressPtclIDs"
polymer2.compressPtclIDs()
print "Testing empty getSubStructure"
subStruc = polymer2.getSubStructure([])
print "subStruc = ", subStruc
print "Testing empty getPtclPositions"
posList = polymer2.getPtclPositions()
print "posList = ", posList
print "------------------------------------------------------------------------------------ \n"
print "Testing struc add --> non-empty (polymer1) += empty (polymer2)"
polymer1 += polymer2
print "polymer1 = ", polymer1
print "------------------------------------------------------------------------------------ \n"
print "polymer2 = ", polymer2
print "------------------------------------------------------------------------------------ \n"
print "Testing struc add --> empty (polymer2) += non-empty (polymer1)"
polymer2 += polymer1
print "polymer2 = ", polymer2
print "------------------------------------------------------------------------------------ \n"
print "polymer1 = ", polymer1
print "------------------------------------------------------------------------------------ \n"
print "Testing empty getSubStructure with non-zero id list (should return ERROR)"
polymer3 = StructureContainer()
subStruc = polymer3.getSubStructure([1, 2])
print "subStruc = ", subStruc