def setUp(self):
from pygmin.potentials import LJ
from pygmin import defaults
from pygmin.mindist import CoMToOrigin
self.natoms = 15
self.pot = LJ(self.natoms)
self.permlist = [range(self.natoms)]
self.X1 = np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3)/2
ret = defaults.quenchRoutine(self.X1, self.pot.getEnergyGradient, tol=.1)
self.X1 = ret[0]
self.X1 = CoMToOrigin(self.X1)
def testGradient(self):
natoms = 10
coords = np.random.uniform(-1, 1, natoms * 3) * 2
lj = LJ()
atlj = ATLJ(Z=3.)
e, Gf = atlj.getEnergyGradientFortran(coords)
e, Gn = atlj.getEnergyGradientNumerical(coords)
print Gf
print Gn
maxdiff = np.max(np.abs(Gf - Gn))
maxnorm = np.max(np.abs(Gf + Gn)) / 2
maxrel = np.max(np.abs((Gf - Gn) / (Gf + Gn) * 2.))
print "maximum relative difference in gradients", maxdiff, maxdiff / maxnorm
self.assertTrue(
maxdiff / maxnorm < 1e-4,
"ATLJ: gradient differs from numerical gradient by %g" % (maxdiff))
def testenergy(self):
natoms = 10
coords = np.random.uniform(-1, 1, natoms * 3) * 2
from pygmin.optimize import mylbfgs as quench
lj = LJ()
ret = quench(coords, lj)
coords = ret.coords
atlj = ATLJ(Z=3.)
e2 = atlj.getEnergySlow(coords)
# e1 = atlj.getEnergyWeave(coords)
# #print "%g - %g = %g" % (e1, e2, e1-e2)
# self.assertTrue( abs(e1 - e2) < 1e-12, "ATLJ: two energy methods give different results: %g - %g = %g" % (e1, e2, e1-e2) )
e1 = atlj.getEnergyFortran(coords)
#print "%g - %g = %g" % (e1, e2, e1-e2)
#print e1/e2
self.assertTrue(
abs(e1 - e2) < 1e-12,
"ATLJ: fortran energy gives different results: %g - %g = %g" %
(e1, e2, e1 - e2))
def mytest(nmin=40, natoms=13):
from pygmin.landscape import DoubleEndedConnect
from pygmin.landscape._graph import create_random_database
from pygmin.mindist import minPermDistStochastic, MinDistWrapper
from pygmin.potentials import LJ
from pygmin.landscape import TSGraph
pot = LJ()
mindist = MinDistWrapper(minPermDistStochastic,
permlist=[range(natoms)],
niter=10)
db = create_random_database(nmin=nmin, natoms=natoms)
min1, min2 = list(db.minima())[:2]
graph = TSGraph(db)
connect = DoubleEndedConnect(min1,
min2,
pot,
mindist,
db,
use_all_min=True,
merge_minima=True,
max_dist_merge=.1)
def getEnergy(self, coords):
atom_coords = self.aatopology.to_atomistic(coords)
return LJ.getEnergy(self, atom_coords.flatten())
def __init__(self, aatopology):
self.aatopology = aatopology
LJ.__init__(self)
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
print len(rbsystem.sites), len(rbsystem.indices)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.indices[0]] - site.atom_positions[0]
# for simplicity just use a lj potential here
pot = LJ(sigma=2.)
# get the flattened coordinate array
print pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
print cg.posRigid
print cg.rotRigid
ret = lbfgs_py(rbcoords.coords, rbpot.getEnergyGradient)
print ret[1]
xyz.write_xyz(open("quenched.xyz", "w"), rbsystem.to_atomistic(ret[0]), atomtypes=ref.atomtypes)
import _pygmin
import numpy as np
import time
import sys
import _lj
import _lbfgs
from pygmin.optimize import mylbfgs
N = 100
natoms = [
10, 13, 20, 30, 31, 38, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140,
150
]
print "benchmarking lennard jones potential, %d atoms, %d calls", natoms, N
pot_old = LJ()
pot = _lj.LJ()
clbfgs = _lbfgs.LBFGS(pot)
res = open("results.txt", "w")
for na in natoms:
t0 = time.time()
for i in xrange(N):
x = np.random.random(3 * na) - 0.5
ret = clbfgs.run(x)
t1 = time.time()
for i in xrange(N):
x = np.random.random(3 * na) - 0.5
class ATLJ(BasePotential):
"""
Lennard Jones + three body Axilrod-Teller term
V = sum_ij VLJ_ij + sum_ijk Z * (1 + 3*cos(t1)*cos(t2)*cos(t3)) / (rij * rjk * rik)**3 )
where t1, t2, t3 are the internal angles of the triangle ijk
Z > 0 stabilizes linear vs. triangular geometries
"""
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
def getEnergyWeave(self, coords):
"""
use weave inline
"""
Elj = self.lj.getEnergy(coords)
natoms = coords.size/3
coords = np.reshape(coords, [natoms,3])
energy=0.
Z = self.Z
#support_code
code = """
double drij[3];
double drik[3];
double drjk[3];
energy = 0.;
for (int i=0; i < natoms; ++i){
for (int j=0; j<i; ++j){
for (int k=0; k<j; ++k){
double rij = 0.;
double rik = 0.;
double rjk = 0.;
for (int d=0; d<3; ++d){
drij[d] = coords(i,d) - coords(j,d);
rij += drij[d]*drij[d];
}
for (int d=0; d<3; ++d){
drjk[d] = coords(j,d) - coords(k,d);
rjk += drjk[d]*drjk[d];
}
for (int d=0; d<3; ++d){
drik[d] = coords(i,d) - coords(k,d);
rik += drik[d]*drik[d];
}
rij = sqrt(rij);
rjk = sqrt(rjk);
rik = sqrt(rik);
double ctijk = ( -(drij[0]*drjk[0] + drij[1]*drjk[1] + drij[2]*drjk[2]) / (rij * rjk) );
double ctjki = ( (drjk[0]*drik[0] + drjk[1]*drik[1] + drjk[2]*drik[2]) / (rjk * rik) );
double ctkij = ( (drik[0]*drij[0] + drik[1]*drij[1] + drik[2]*drij[2]) / (rik * rij) );
double r3 = rij*rjk*rik;
energy += Z*(1. + 3. * ctijk * ctjki * ctkij) / (r3*r3*r3);
}
}
}
return_val= energy;
"""
energy = weave.inline(code, ["coords", "energy", "Z", "natoms"], type_converters=converters.blitz, verbose=2)
#print "fast energy", Elj, energy
energy += Elj
return energy
def getEnergySlow(self, coords):
Elj = self.lj.getEnergy(coords)
natoms = coords.size/3
X = np.reshape(coords, [natoms,3])
Z = self.Z
energy = 0.
for i in range(natoms):
for j in range(i):
for k in range(j):
#print i, j, k
drij = X[i,:] - X[j,:]
drik = X[i,:] - X[k,:]
drjk = X[j,:] - X[k,:]
rij = np.linalg.norm( drij )
rik = np.linalg.norm( drik )
rjk = np.linalg.norm( drjk )
energy += Z * (1. + 3.*\
np.dot( drij, -drjk ) * \
np.dot(-drij, -drik ) * \
np.dot( drik, drjk ) / (rij*rik*rjk)**2) \
/ (rij*rik*rjk)**3
#print "slow energy", Elj, energy
energy += Elj
return energy
def getEnergyFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords)/3
garbage, e = ATfort.axt(coords, False, self.Z, [natoms])
Elj = self.lj.getEnergy(coords)
return e + Elj
def getEnergyGradientFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords)/3
grad, e = ATfort.axt(coords, True, self.Z, [natoms])
elj, gradlj = self.lj.getEnergyGradient(coords)
return e + elj, grad + gradlj
def getEnergy(self, coords):
return self.getEnergyFortran(coords)
def getEnergyGradient(self, coords):
#return self.getEnergyGradientNumerical(coords)
return self.getEnergyGradientFortran(coords)
def getEnergy(self, coords):
atom_coords = self.aatopology.to_atomistic(coords)
return LJ.getEnergy(self, atom_coords.flatten())
# benchmark all interface
from pygmin.potentials import LJ
import _pygmin
import numpy as np
import time
import sys
import _lj
import _lbfgs
from pygmin.optimize import mylbfgs
N=10 # int(sys.argv[2])
natoms=38 #int(sys.argv[1])
print "benchmarking lennard jones potential, %d atoms, %d calls", natoms, N
pot_old = LJ()
pot = _lj.LJ()
clbfgs = _lbfgs.LBFGS(pot)
t0 = time.time()
for i in xrange(100):
x = 1.*(np.random.random(3*natoms) - 0.5)
ret = clbfgs.run(x)
#print ret
#print ret[0]
#print pot.get_energy(ret[0])
e, g = pot.get_energy_gradient(ret[0])
print "C", np.linalg.norm(g)
t1 = time.time()
for i in xrange(100):
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
class ATLJ(BasePotential):
"""
Lennard Jones + three body Axilrod-Teller term
V = sum_ij VLJ_ij + sum_ijk Z * (1 + 3*cos(t1)*cos(t2)*cos(t3)) / (rij * rjk * rik)**3 )
where t1, t2, t3 are the internal angles of the triangle ijk
Z > 0 stabilizes linear vs. triangular geometries
"""
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
def getEnergyWeave(self, coords):
"""
use weave inline
"""
Elj = self.lj.getEnergy(coords)
natoms = coords.size / 3
coords = np.reshape(coords, [natoms, 3])
energy = 0.
Z = self.Z
#support_code
code = """
double drij[3];
double drik[3];
double drjk[3];
energy = 0.;
for (int i=0; i < natoms; ++i){
for (int j=0; j<i; ++j){
for (int k=0; k<j; ++k){
double rij = 0.;
double rik = 0.;
double rjk = 0.;
for (int d=0; d<3; ++d){
drij[d] = coords(i,d) - coords(j,d);
rij += drij[d]*drij[d];
}
for (int d=0; d<3; ++d){
drjk[d] = coords(j,d) - coords(k,d);
rjk += drjk[d]*drjk[d];
}
for (int d=0; d<3; ++d){
drik[d] = coords(i,d) - coords(k,d);
rik += drik[d]*drik[d];
}
rij = sqrt(rij);
rjk = sqrt(rjk);
rik = sqrt(rik);
double ctijk = ( -(drij[0]*drjk[0] + drij[1]*drjk[1] + drij[2]*drjk[2]) / (rij * rjk) );
double ctjki = ( (drjk[0]*drik[0] + drjk[1]*drik[1] + drjk[2]*drik[2]) / (rjk * rik) );
double ctkij = ( (drik[0]*drij[0] + drik[1]*drij[1] + drik[2]*drij[2]) / (rik * rij) );
double r3 = rij*rjk*rik;
energy += Z*(1. + 3. * ctijk * ctjki * ctkij) / (r3*r3*r3);
}
}
}
return_val= energy;
"""
energy = weave.inline(code, ["coords", "energy", "Z", "natoms"],
type_converters=converters.blitz,
verbose=2)
#print "fast energy", Elj, energy
energy += Elj
return energy
def getEnergySlow(self, coords):
Elj = self.lj.getEnergy(coords)
natoms = coords.size / 3
X = np.reshape(coords, [natoms, 3])
Z = self.Z
energy = 0.
for i in range(natoms):
for j in range(i):
for k in range(j):
#print i, j, k
drij = X[i, :] - X[j, :]
drik = X[i, :] - X[k, :]
drjk = X[j, :] - X[k, :]
rij = np.linalg.norm(drij)
rik = np.linalg.norm(drik)
rjk = np.linalg.norm(drjk)
energy += Z * (1. + 3.*\
np.dot( drij, -drjk ) * \
np.dot(-drij, -drik ) * \
np.dot( drik, drjk ) / (rij*rik*rjk)**2) \
/ (rij*rik*rjk)**3
#print "slow energy", Elj, energy
energy += Elj
return energy
def getEnergyFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords) / 3
garbage, e = ATfort.axt(coords, False, self.Z, [natoms])
Elj = self.lj.getEnergy(coords)
return e + Elj
def getEnergyGradientFortran(self, coords):
#grad,potel = axt(x,gradt,zstar,[n])
natoms = len(coords) / 3
grad, e = ATfort.axt(coords, True, self.Z, [natoms])
elj, gradlj = self.lj.getEnergyGradient(coords)
return e + elj, grad + gradlj
def getEnergy(self, coords):
return self.getEnergyFortran(coords)
def getEnergyGradient(self, coords):
#return self.getEnergyGradientNumerical(coords)
return self.getEnergyGradientFortran(coords)
def get_potential(self):
return LJ(self.natoms)
def getEnergyGradient(self, coords):
atom_coords = self.aatopology.to_atomistic(coords)
e, atom_grad = LJ.getEnergyGradient(self, atom_coords.flatten())
grad = self.aatopology.transform_gradient(coords, atom_grad)
return e, grad
def __init__(self, aatopology):
self.aatopology = aatopology
LJ.__init__(self)
# benchmark all interface
from pygmin.potentials import LJ
import _pygmin
import numpy as np
import time
import sys
import _lj
import _lbfgs
from pygmin.optimize import mylbfgs
N = 10 # int(sys.argv[2])
natoms = 38 #int(sys.argv[1])
print "benchmarking lennard jones potential, %d atoms, %d calls", natoms, N
pot_old = LJ()
pot = _lj.LJ()
clbfgs = _lbfgs.LBFGS(pot)
t0 = time.time()
for i in xrange(100):
x = 1. * (np.random.random(3 * natoms) - 0.5)
ret = clbfgs.run(x)
#print ret
#print ret[0]
#print pot.get_energy(ret[0])
e, g = pot.get_energy_gradient(ret[0])
print "C", np.linalg.norm(g)
t1 = time.time()
for i in xrange(100):
def getEnergyGradient(self, coords):
atom_coords = self.aatopology.to_atomistic(coords)
e, atom_grad = LJ.getEnergyGradient(self, atom_coords.flatten())
grad = self.aatopology.transform_gradient(coords, atom_grad)
return e, grad
# finalize the rigid body setup
for rb in rb_sites:
rb.finalize_setup()
# define a new rigid body system
rbsystem = rigidbody.RBSystem()
rbsystem.add_sites(rb_sites)
print len(rbsystem.sites), len(rbsystem.indices)
rbcoords = rbsystem.coords_adapter(np.zeros(len(rbsystem.sites)*6))
for site, com in zip(rbsystem.sites, rbcoords.posRigid):
com[:] = ref.coords[site.indices[0]] - site.atom_positions[0]
# for simplicity just use a lj potential here
pot = LJ(sigma=2.)
# get the flattened coordinate array
print pot.getEnergy(ref.coords.flatten())
rbpot = rigidbody.RBPotentialWrapper(rbsystem, pot)
print rbpot.getEnergy(rbcoords.coords)
e, g = rbpot.getEnergyGradient(rbcoords.coords)
g_n = rbpot.NumericalDerivative(rbcoords.coords, eps=1e-4)
cg = rbsystem.coords_adapter(g-g_n)
print cg.posRigid
print cg.rotRigid
ret = lbfgs_py(rbcoords.coords, rbpot)
print ret.energy
xyz.write_xyz(open("quenched.xyz", "w"), rbsystem.to_atomistic(ret.coords), atomtypes=ref.atomtypes)
def __init__(self, eps=1.0, sig=1.0, Z=1.):
""" simple lennard jones potential"""
self.sig = sig
self.eps = eps
self.Z = Z
self.lj = LJ(self.sig, self.eps)
def get_potential(self):
return LJ()