def test_molecule():
otp = setupLWOTP()
xyz = otp.getxyz()
from pele.printing.print_atoms_xyz import printAtomsXYZ as printxyz
import sys
#with open("out.xyz", "w") as fout:
printxyz(sys.stdout, xyz)
aa = np.array([.2, .3, .4])
for xyz, aanew in otp.getSymmetries( np.zeros(3), aa):
printxyz(sys.stdout, xyz, line2="symmetry")
xyz = otp.getxyz(aa = aanew)
printxyz(sys.stdout, xyz, line2="symmetry from returned aa")
def test_sandbox(nmol = 6):
import copy
from pele.potentials.lj import LJ
#define the molecule types.
#here use only one type, LWOTP
otp = molecule.setupLWOTP()
# define the interaction matrix for the system.
# for LWOTP there is only one atom type, so this is trivial
lj = LJ()
interaction_matrix = [[lj]]
#set up a list of molecules
mols = [otp for i in range(nmol)]
#set up the RBSandbox object
mysys = RBSandbox(mols, interaction_matrix)
nsites = mysys.nsites
#get an initial set of coordinates
comcoords = np.random.uniform(-1,1,[nmol*3]) * 1.3*(nsites)**(1./3)
aacoords = np.array( [copy.copy(rot.random_aa()) for i in range(nmol)] )
aacoords = aacoords.reshape(3*nmol)
coords = np.zeros(2*3*nmol, np.float64)
coords[0:3*nmol] = comcoords[:]
coords[3*nmol:2*3*nmol] = aacoords[:]
print "lencoords, len aacoords", len (coords), len(aacoords), len(comcoords)
#print "xyz coords", mysys.transformToXYZ(coords)
#save the initial set of coords
printlist = []
xyz = mysys.getxyz( coords )
printlist.append( (xyz.copy(), "initial"))
#calculate the initial energy
Einit = mysys.getEnergy(coords)
print "initial energy", Einit
#test the gradient
numericV = mysys.NumericalDerivative(coords, 1e-10)
numericV = numericV.copy()
print "numeric V", numericV
E, V = mysys.getEnergyGradient(coords)
print "energy from gradient", E, "difference", E - Einit
#print "analytic gradient", V
maxgrad_relative = np.max(np.abs(V-numericV)/np.abs(V))
maxgraddiff = np.max(np.abs(V - numericV))
print "max error in gradient", maxgraddiff, "max relative", maxgrad_relative
#do a quench to make sure everything is working well
from pele.optimize import lbfgs_scipy
coords, E, rms, funcalls = lbfgs_scipy(coords, mysys.getEnergyGradient, iprint=-1)
print "postquench E", E, "rms", rms, "funtion calls", funcalls
xyz = mysys.getxyz(coords )
printlist.append( (xyz.copy(), "post quench"))
#print the saved coords
fname = "otp.xyz"
print "saving xyz coords to", fname
from pele.printing.print_atoms_xyz import printAtomsXYZ as printxyz
with open(fname, "w") as fout:
for xyz, line2 in printlist:
printxyz( fout, xyz, line2=line2, atom_type=["N", "O", "O"])
test_symmetries(coords, mysys)