def test(X1, X2, lj, atomtypes=None, fname="lj.xyz", minPermDist=MinPermDistCluster()): # pragma: no cover
if not atomtypes: atomtypes = ["LA"]
import copy
natoms = len(X1) / 3
X1i = copy.copy(X1)
X2i = copy.copy(X2)
printlist = []
printlist.append((X2.copy(), "X2 initial"))
printlist.append((X1.copy(), "X1 initial"))
distinit = np.linalg.norm(X1-X2)
print "distinit", distinit
(dist, X1, X2) = minPermDist(X1,X2)
distfinal = np.linalg.norm(X1-X2)
print "dist returned ", dist
print "dist from coords ", distfinal
print "initial energies (post quench)", lj.getEnergy(X1i), lj.getEnergy(X2i)
print "final energies ", lj.getEnergy(X1), lj.getEnergy(X2)
printlist.append((X1.copy(), "X1 final"))
printlist.append((X2.copy(), "X2 final"))
import pele.printing.print_atoms_xyz as printxyz
with open(fname, "w") as fout:
for xyz, line2 in printlist:
printxyz.printAtomsXYZ(fout, xyz, line2=line2 +" "+ str(lj.getEnergy(xyz)))
def test(X1, X2, lj, atomtypes=["LA"], permlist = None, fname = "lj.xyz",
minPermDist=minPermDistStochastic):
import copy
natoms = len(X1) / 3
if permlist == None:
permlist = [range(natoms)]
X1i = copy.copy(X1)
X2i = copy.copy(X2)
printlist = []
printlist.append((X2.copy(), "X2 initial"))
printlist.append((X1.copy(), "X1 initial"))
distinit = np.linalg.norm(X1-X2)
print "distinit", distinit
(dist, X1, X2) = minPermDist(X1,X2, permlist=permlist)
distfinal = np.linalg.norm(X1-X2)
print "dist returned ", dist
print "dist from coords ", distfinal
print "initial energies (post quench)", lj.getEnergy(X1i), lj.getEnergy(X2i)
print "final energies ", lj.getEnergy(X1), lj.getEnergy(X2)
printlist.append((X1.copy(), "X1 final"))
printlist.append((X2.copy(), "X2 final"))
import pele.printing.print_atoms_xyz as printxyz
with open(fname, "w") as fout:
for xyz, line2 in printlist:
printxyz.printAtomsXYZ(fout, xyz, line2=line2 +" "+ str(lj.getEnergy(xyz)))
def test(coords1, coords2, mysys, permlist):
printlist = []
printlist.append((coords1.copy(), "after quench"))
printlist.append((coords2.copy(), "after quench"))
coords2in = coords2.copy()
coords1in = coords1.copy()
distinit = getDistaa(coords1, coords2, mysys)
print "distinit", distinit
(dist, coords1, coords2) = minPermDistRBMol(coords1, coords2, mysys, permlist=permlist)
distfinal = getDistaa(coords1, coords2, mysys)
print "dist returned ", dist
print "dist from coords ", distfinal
print "coords2 initial energy", mysys.getEnergy(coords2in)
print "coords2 final energy ", mysys.getEnergy(coords2)
print "coords1 initial energy", mysys.getEnergy(coords1in)
print "coords1 final energy ", mysys.getEnergy(coords1)
printlist.append((coords1.copy(), "coords1 after mindist"))
printlist.append((coords2.copy(), "coords2 after mindist"))
import pele.printing.print_atoms_xyz as printxyz
with open("otp.xyz", "w") as fout:
for coords, line2 in printlist:
xyz = mysys.getxyz(coords)
printxyz.printAtomsXYZ(fout, xyz, line2=line2, atom_type=["N", "O", "O"])
return dist, coords1, coords2
def main():
natoms = 9
X1 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
X2 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
#X1 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 0., 1.,] )
#X2 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 1., 0.,] )
import copy
X1i = copy.copy(X1)
X2i = copy.copy(X2)
distinit = np.linalg.norm(X1-X2)
print "distinit", distinit
(dist, X1, X2) = minPermDistLong(X1,X2)
distfinal = np.linalg.norm(X1-X2)
print "dist returned ", dist
print "dist from coords ", distfinal
import pele.printing.print_atoms_xyz as printxyz
with open("out.xyz", "w") as fout:
CoMToOrigin(X1i)
CoMToOrigin(X2i)
printxyz.printAtomsXYZ(fout, X1i )
printxyz.printAtomsXYZ(fout, X2i )
printxyz.printAtomsXYZ(fout, X1 )
printxyz.printAtomsXYZ(fout, X2 )
def test(X1,
X2,
lj,
atomtypes=None,
fname="lj.xyz",
minPermDist=MinPermDistCluster()): # pragma: no cover
if not atomtypes: atomtypes = ["LA"]
import copy
natoms = len(X1) / 3
X1i = copy.copy(X1)
X2i = copy.copy(X2)
printlist = []
printlist.append((X2.copy(), "X2 initial"))
printlist.append((X1.copy(), "X1 initial"))
distinit = np.linalg.norm(X1 - X2)
print("distinit", distinit)
(dist, X1, X2) = minPermDist(X1, X2)
distfinal = np.linalg.norm(X1 - X2)
print("dist returned ", dist)
print("dist from coords ", distfinal)
print("initial energies (post quench)", lj.getEnergy(X1i),
lj.getEnergy(X2i))
print("final energies ", lj.getEnergy(X1), lj.getEnergy(X2))
printlist.append((X1.copy(), "X1 final"))
printlist.append((X2.copy(), "X2 final"))
import pele.printing.print_atoms_xyz as printxyz
with open(fname, "w") as fout:
for xyz, line2 in printlist:
printxyz.printAtomsXYZ(fout,
xyz,
line2=line2 + " " + str(lj.getEnergy(xyz)))
