def lbfgs_py(coords, pot, **kwargs):
if not hasattr(pot, "getEnergyGradient"):
# for compatibility with old quenchers.
# assume pot is a getEnergyGradient function
pot = _getEnergyGradientWrapper(pot)
lbfgs = LBFGS(coords, pot, **kwargs)
return lbfgs.run()
def lbfgs_py(coords, pot, **kwargs):
if not hasattr(pot, "getEnergyGradient"):
# for compatibility with old quenchers.
# assume pot is a getEnergyGradient function
pot = _getEnergyGradientWrapper(pot)
lbfgs = LBFGS(coords, pot, **kwargs)
return lbfgs.run()
def runtest(X, pot, natoms = 100, iprint=-1):
from _lbfgs_py import PrintEvent
tol = 1e-5
maxstep = 0.005
Xinit = np.copy(X)
e, g = pot.getEnergyGradient(X)
print "energy", e
lbfgs = LBFGS(X, pot, maxstep = 0.1, nsteps=10000, tol=tol,
iprint=iprint, H0=2.)
printevent = PrintEvent( "debugout.xyz")
lbfgs.attachEvent(printevent)
ret = lbfgs.run()
print ret
print ""
print "now do the same with scipy lbfgs"
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(Xinit, pot, tol = tol)
print ret
#print ret[1], ret[2], ret[3]
if False:
print "now do the same with scipy bfgs"
from pygmin.optimize import bfgs as oldbfgs
ret = oldbfgs(Xinit, pot, tol = tol)
print ret
if False:
print "now do the same with gradient + linesearch"
import _bfgs
gpl = _bfgs.GradientPlusLinesearch(Xinit, pot, maxstep = 0.1)
ret = gpl.run(1000, tol = 1e-6)
print ret
if False:
print "calling from wrapper function"
from pygmin.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol = tol)
print ret
if True:
print ""
print "now do the same with lbfgs_py"
from pygmin.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol = tol)
print ret
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
for n, coords in enumerate(printevent.coordslist):
coords=coords.reshape(natoms, 3)
pym.draw_spheres(coords, "A", n)
except ImportError:
print "error loading pymol"
def _lbfgs_py(coords, pot, **kwargs):
lbfgs = LBFGS(coords, pot, **kwargs)
ret = lbfgs.run()
coords = ret.coords
e = ret.energy
rms = ret.rms
funcalls = ret.nfev
return coords, e, rms, funcalls, ret
def _lbfgs_py(coords, pot, **kwargs):
lbfgs = LBFGS(coords, pot, **kwargs)
ret = lbfgs.run()
coords = ret.coords
e = ret.energy
rms = ret.rms
funcalls = ret.nfev
return coords, e, rms, funcalls, ret
def runtest(X, pot, natoms=100, iprint=-1):
from _lbfgs_py import PrintEvent
tol = 1e-5
maxstep = 0.005
Xinit = np.copy(X)
e, g = pot.getEnergyGradient(X)
print "energy", e
lbfgs = LBFGS(X,
pot,
maxstep=0.1,
nsteps=10000,
tol=tol,
iprint=iprint,
H0=2.)
printevent = PrintEvent("debugout.xyz")
lbfgs.attachEvent(printevent)
ret = lbfgs.run()
print ret
print ""
print "now do the same with scipy lbfgs"
from pygmin.optimize import lbfgs_scipy as quench
ret = quench(Xinit, pot, tol=tol)
print ret
#print ret[1], ret[2], ret[3]
if False:
print "now do the same with scipy bfgs"
from pygmin.optimize import bfgs as oldbfgs
ret = oldbfgs(Xinit, pot, tol=tol)
print ret
if False:
print "now do the same with gradient + linesearch"
import _bfgs
gpl = _bfgs.GradientPlusLinesearch(Xinit, pot, maxstep=0.1)
ret = gpl.run(1000, tol=1e-6)
print ret
if False:
print "calling from wrapper function"
from pygmin.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol=tol)
print ret
if True:
print ""
print "now do the same with lbfgs_py"
from pygmin.optimize import lbfgs_py
ret = lbfgs_py(Xinit, pot, tol=tol)
print ret
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
for n, coords in enumerate(printevent.coordslist):
coords = coords.reshape(natoms, 3)
pym.draw_spheres(coords, "A", n)
except ImportError:
print "error loading pymol"