class LJCutTest(unittest.TestCase):
def setUp(self):
self.natoms = 10
self.coords = np.random.uniform(-1,1.,3*self.natoms) * self.natoms**(-1./3)
self.pot = LJCut()
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
import itertools
self.ilist = [] #np.zeros([self.natoms*(self.natoms-1)/2, 2])
k = 0
for i in range(self.natoms):
for j in range(i):
k += 1
self.ilist.append( [i,j] )
self.ilist = np.array(self.ilist)
#print self.ilist
def test_grad_e(self):
self.assertAlmostEqual(self.E, self.Egrad, 7)
def test_lists_e(self):
e = self.pot.getEnergyList(self.coords, self.ilist)
self.assertAlmostEqual(self.E, e, 7)
def test_lists_eg(self):
e, g = self.pot.getEnergyGradientList(self.coords, self.ilist)
self.assertAlmostEqual(self.E, e, 7)
gdiffmax = np.max(np.abs( g-self.grad )) / np.max(np.abs(self.grad))
self.assertLess(gdiffmax, 1e-7)
class LJCutTest(unittest.TestCase):
def setUp(self):
self.natoms = 10
self.coords = np.random.uniform(
-1, 1., 3 * self.natoms) * self.natoms**(-1. / 3)
self.pot = LJCut()
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
self.ilist = [] # np.zeros([self.natoms*(self.natoms-1)/2, 2])
k = 0
for i in range(self.natoms):
for j in range(i):
k += 1
self.ilist.append([i, j])
self.ilist = np.array(self.ilist)
# print self.ilist
def test_grad_e(self):
self.assertAlmostEqual(self.E, self.Egrad, 7)
def test_lists_e(self):
e = self.pot.getEnergyList(self.coords, self.ilist)
self.assertAlmostEqual(self.E, e, 7)
def test_lists_eg(self):
e, g = self.pot.getEnergyGradientList(self.coords, self.ilist)
self.assertAlmostEqual(self.E, e, 7)
gdiffmax = np.max(np.abs(g - self.grad)) / np.max(np.abs(self.grad))
self.assertLess(gdiffmax, 1e-7)
def setUp(self):
self.natoms = 10
self.coords = np.random.uniform(
-1, 1., 3 * self.natoms) * self.natoms**(-1. / 3)
self.pot = LJCut()
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
self.ilist = [] # np.zeros([self.natoms*(self.natoms-1)/2, 2])
k = 0
for i in range(self.natoms):
for j in range(i):
k += 1
self.ilist.append([i, j])
self.ilist = np.array(self.ilist)
def setUp(self):
self.natoms = 10
self.coords = np.random.uniform(-1, 1., 3 * self.natoms) * self.natoms ** (-1. / 3)
self.pot = LJCut()
self.E = self.pot.getEnergy(self.coords)
self.Egrad, self.grad = self.pot.getEnergyGradient(self.coords)
self.ilist = [] # np.zeros([self.natoms*(self.natoms-1)/2, 2])
k = 0
for i in range(self.natoms):
for j in range(i):
k += 1
self.ilist.append([i, j])
self.ilist = np.array(self.ilist)
def makeBLJNeighborListPotFreeze(natoms,
frozenlist,
ntypeA=None,
rcut=2.5,
boxl=None):
"""
create the potential object for the kob andersen binary lennard jones with frozeen particles
Parameters
----------
natoms :
number of atoms in the system
frozenlist :
list of frozen atoms
ntypeA :
number of atoms of type A. It is assumed that they have indices in [0,ntypeA]
rcut :
the cutoff for the lj potential in units of sigA
boxl :
the box length for periodic box. None for no periodic boundary conditions
"""
print "making BLJ neighborlist potential", natoms, ntypeA, rcut, boxl
if ntypeA is None:
ntypeA = int(natoms * 0.8)
Alist = range(ntypeA)
Blist = range(ntypeA, natoms)
frozenA = np.array([i for i in Alist if i in frozenlist])
mobileA = np.array([i for i in Alist if i not in frozenlist])
frozenB = np.array([i for i in Blist if i in frozenlist])
mobileB = np.array([i for i in Blist if i not in frozenlist])
blj = ljpshift.LJpshift(natoms, ntypeA, rcut=rcut)
ljAA = LJCut(eps=blj.AA.eps,
sig=blj.AA.sig,
rcut=rcut * blj.AA.sig,
boxl=boxl)
ljBB = LJCut(eps=blj.BB.eps,
sig=blj.BB.sig,
rcut=rcut * blj.BB.sig,
boxl=boxl)
ljAB = LJCut(eps=blj.AB.eps,
sig=blj.AB.sig,
rcut=rcut * blj.AB.sig,
boxl=boxl)
# ten lists in total
# nlAA_ff
# nlAA_mm
# nlAA_mf
# nlBB_ff
# nlBB_mm
# nlBB_mf
# nlAB_ff
# nlAB_mm
# nlAB_mf
# nlAB_fm
nlAA_ff = NeighborListSubsetBuild(natoms, rcut, frozenA, boxl=boxl)
nlAA_mm = NeighborListSubsetBuild(natoms, rcut, mobileA, boxl=boxl)
nlAA_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=frozenA,
boxl=boxl)
nlBB_ff = NeighborListSubsetBuild(natoms, rcut, frozenB, boxl=boxl)
nlBB_mm = NeighborListSubsetBuild(natoms, rcut, mobileB, boxl=boxl)
nlBB_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileB,
Blist=frozenB,
boxl=boxl)
nlAB_ff = NeighborListSubsetBuild(natoms,
rcut,
frozenA,
Blist=frozenB,
boxl=boxl)
nlAB_mm = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=mobileB,
boxl=boxl)
nlAB_mf = NeighborListSubsetBuild(natoms,
rcut,
mobileA,
Blist=frozenB,
boxl=boxl)
nlAB_fm = NeighborListSubsetBuild(natoms,
rcut,
mobileB,
Blist=frozenA,
boxl=boxl)
potlist_frozen = [
NeighborListPotentialBuild(nlAA_ff, ljAA),
NeighborListPotentialBuild(nlBB_ff, ljBB),
NeighborListPotentialBuild(nlAB_ff, ljAB)
]
potlist_mobile = [
NeighborListPotentialBuild(nlAA_mm, ljAA),
NeighborListPotentialBuild(nlAA_mf, ljAA),
NeighborListPotentialBuild(nlBB_mm, ljBB),
NeighborListPotentialBuild(nlBB_mf, ljBB),
NeighborListPotentialBuild(nlAB_mm, ljAB),
NeighborListPotentialBuild(nlAB_mf, ljAB),
NeighborListPotentialBuild(nlAB_fm, ljAB),
]
# wrap the mobile potentials so the check for whether coords needs to be updated
# can be done all at once
mobile_pot = NeighborListPotentialMulti(potlist_mobile,
natoms,
rcut,
boxl=boxl)
# wrap the mobile and frozen potentials together
mcpot = MultiComponentSystemFreeze([mobile_pot], potlist_frozen)
# finally, wrap it once more in a class that will zero the gradients of the frozen atoms
frozenpot = FreezePot(mcpot, frozenlist, natoms)
return frozenpot
