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 pygmin.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 test(X1, X2, lj, atomtypes=["LA"], fname = "lj.xyz",
minPermDist=MinPermDistCluster()):
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 pygmin.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 pygmin.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 = 5
X1 = np.random.uniform(-1, 1, [natoms * 3]) * (float(natoms)) ** (1.0 / 3)
X2 = np.random.uniform(-1, 1, [natoms * 3]) * (float(natoms)) ** (1.0 / 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 = minDist(X1, X2)
distfinal = np.linalg.norm(X1 - X2)
print "dist from eigenvalue", dist
print "distfinal", distfinal
import pygmin.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 main():
natoms = 5
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 = minDist(X1,X2)
distfinal = np.linalg.norm(X1-X2)
print "dist from eigenvalue", dist
print "distfinal", distfinal
import pygmin.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 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 pygmin.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=["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 pygmin.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)))
import numpy as np
import pygmin.basinhopping as bh
from pygmin.optimize import _quench as quench
from pygmin.takestep import displace
# export PYTHONPATH=/home/ss2029/svn/GMIN/bin:$PWD/../..
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN)
coords = pot.getCoords()
step = displace.RandomDisplacement(stepsize=0.7)
opt = bh.BasinHopping(coords,
pot,
takeStep=step,
quenchRoutine=quench.lbfgs_py)
opt.quenchParameters['tol'] = 1e-4
opt.run(3)
# some visualization
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(opt.coords, "A", 1)
except:
print "Could not draw using pymol, skipping this step"
import pygmin.printing.print_atoms_xyz as pr
pr.printAtomsXYZ(open("final.xyz", "w"), opt.coords)
import ambgmin_ as GMIN
import pygmin.potentials.gminpotential as gminpot
import numpy as np
import pygmin.basinhopping as bh
from pygmin.optimize import _quench as quench
from pygmin.takestep import displace
# export PYTHONPATH=/home/ss2029/svn/GMIN/bin:$PWD/../..
GMIN.initialize()
pot = gminpot.GMINPotental(GMIN)
coords = pot.getCoords()
step = displace.RandomDisplacement(stepsize=0.7)
opt = bh.BasinHopping(coords, pot, takeStep=step, quenchRoutine=quench.lbfgs_py)
opt.quenchParameters['tol'] = 1e-4
opt.run(3)
# some visualization
try:
import pygmin.utils.pymolwrapper as pym
pym.start()
pym.draw_spheres(opt.coords, "A", 1)
except:
print "Could not draw using pymol, skipping this step"
import pygmin.printing.print_atoms_xyz as pr
pr.printAtomsXYZ(open("final.xyz", "w"), opt.coords)
