def optimize(method,
assert_convergence=ASSERT_CONV,
include_ghost=INCLUDE_GHOST,
**kwargs):
'''Optimize the geometry with the given method.
'''
mol = copy.copy(method.mol)
if 'log' in kwargs:
log = lib.logger.new_logger(method, kwargs['log'])
elif 'verbose' in kwargs:
log = lib.logger.new_logger(method, kwargs['verbose'])
else:
log = lib.logger.new_logger(method)
# geom = optimize_berny(as_berny_solver(method), to_berny_geom(mol),
# log=to_berny_log(log), **kwargs)
# temporary interface, taken from berny.py optimize function
log = to_berny_log(log)
solver = as_berny_solver(method, assert_convergence, include_ghost)
geom = to_berny_geom(mol, include_ghost)
next(solver)
optimizer = Berny(geom, log=log, **kwargs)
for geom in optimizer:
energy, gradients = solver.send(geom)
optimizer.send((energy, gradients))
mol.set_geom_(_geom_to_atom(mol, geom, include_ghost), unit='Bohr')
return mol
def optimize(method,
assert_convergence=ASSERT_CONV,
include_ghost=INCLUDE_GHOST,
callback=None,
**kwargs):
'''Optimize the geometry with the given method.
'''
mol = method.mol.copy()
if 'log' in kwargs:
log = lib.logger.new_logger(method, kwargs['log'])
elif 'verbose' in kwargs:
log = lib.logger.new_logger(method, kwargs['verbose'])
else:
log = lib.logger.new_logger(method)
# temporary interface, taken from berny.py optimize function
berny_log = to_berny_log(log)
solver = as_berny_solver(method, assert_convergence, include_ghost)
geom = to_berny_geom(mol, include_ghost)
optimizer = Berny(geom, log=berny_log, **kwargs)
e_last = 0
for cycle, geom in enumerate(optimizer):
if log.verbose >= lib.logger.NOTE:
log.note('\nGeometry optimization cycle %d', cycle + 1)
_dump_mol_geometry(mol, geom, log)
mol.set_geom_(_geom_to_atom(mol, geom, include_ghost), unit='Bohr')
energy, gradients = solver(mol)
log.note('cycle %d: E = %.12g dE = %g norm(grad) = %g', cycle + 1,
energy, energy - e_last, numpy.linalg.norm(gradients))
e_last = energy
optimizer.send((energy, gradients))
if callable(callback):
callback(locals())
return mol
def optimize(method, **kwargs):
'''Optimize the geometry with the given method.
'''
mol = copy.copy(method.mol)
if 'log' in kwargs:
log = lib.logger.new_logger(method, kwargs['log'])
elif 'verbose' in kwargs:
log = lib.logger.new_logger(method, kwargs['verbose'])
else:
log = lib.logger.new_logger(method)
# geom = optimize_berny(as_berny_solver(method), to_berny_geom(mol),
# log=to_berny_log(log), **kwargs)
# temporary interface, taken from berny.py optimize function
log = to_berny_log(log)
solver = as_berny_solver(method, kwargs.get('assert_convergence', False))
geom = to_berny_geom(mol)
next(solver)
optimizer = Berny(geom, log=log, **kwargs)
for geom in optimizer:
energy, gradients = solver.send(list(geom))
optimizer.send((energy, gradients))
mol.set_geom_(geom_to_atom(geom))
return mol
def get_berny(args):
geom = geomlib.load(sys.stdin, args.format)
if args.paramfile:
with open(args.paramfile) as f:
params = json.load(f)
else:
params = None
berny = Berny(geom, **params)
next(berny)
return berny
def optimize(self, solver):
mol = self.mol_origin
geom_outer = self.mol_to_geom(mol)
optimizer = Berny(geom_outer,
verbosity=(2 + LOGLEVEL),
gradientmax=self.gradientmax,
gradientrms=self.gradientrms,
stepmax=self.stepmax,
steprms=self.steprms)
for geom in optimizer:
mol_opt = self.geom_to_mol(mol, geom)
print("In optimization: Molecular geom")
print(mol_opt.atom_coords() * lib.param.BOHR)
energy, gradients = solver(mol_opt)
optimizer.send((energy, gradients))
geom_outer = geom
return self.geom_to_mol(mol, geom_outer)
def run(self):
if self.optg_berny:
# now optg
gconv = self.gconvs_berny[self.param['gconv']]
gradientmax, gradientrms, stepmax, steprms = [ gconv[k] \
for k in ['gradientmax', 'gradientrms', 'stepmax', 'steprms'] ]
optimizer = Berny(geomlib.readfile(self.fn+'.xyz'), \
gradientmax = gradientmax, \
gradientrms = gradientrms, \
steprms=steprms, stepmax=stepmax, \
maxsteps=self.param['maxit'])
solver = self.get_energy_and_gradient()
next(solver)
coords_a = []
es_a = []
grads_a = []
idx = 0
for geom in optimizer:
atoms = list(geom)
if not isinstance(atoms[0], tuple):
atoms = atoms[-1]
print(' * idx = ', idx)
#if idx == 0 and (self.gradients is not None):
# energy, gradients = self.energy, self.gradients
#else:
energy, gradients = solver.send((atoms, None))
coords_a.append(geom.coords)
es_a.append(energy)
grads_a.append(gradients)
idx += 1
optimizer.send((energy, gradients))
self.coords_a = coords_a
self.grads_a = grads_a
self.es_a = es_a
self.coords = coords_a[-1]
self.gradients = grads_a[-1]
self.energy = es_a[-1]
else:
mol = cc.molecules(self.fn + '.xyz')
gmol = cmc.RawMol(mol)
self.get_energy(gmol)
def test_cyanogen(mopac, cyanogen):
berny = Berny(cyanogen, steprms=0.01, stepmax=0.05, maxsteps=4)
final = optimize(berny, mopac)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([0, 107.5, 107.5], rel=1e-3, abs=1e-3)
def test_aniline(mopac, aniline):
berny = Berny(aniline, steprms=0.01, stepmax=0.05, maxsteps=8)
final = optimize(berny, mopac)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([90.94, 193.1, 283.9], rel=1e-3)
def test_ethanol(mopac, ethanol):
berny = Berny(ethanol, steprms=0.01, stepmax=0.05, maxsteps=5)
final = optimize(berny, mopac)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([14.95, 52.58, 61.10], rel=1e-3)
time.sleep(30)
print("done sleeping")
pass
#load in the etot and gtot
etot = np.load('energy.npy')
gtot = np.load('gradient.npy')
print("energy from .npy = ", etot)
os.chdir('../')
return etot, gtot
#start of pyberny optimizer
obj_list[0].write_xyz(coords_name)
os.path.abspath(os.curdir)
optimizer = Berny(geomlib.readfile(os.path.abspath(coords_name)), debug=True)
count = 0
etot_opt = 0
grad_opt = 0
for geom in optimizer:
print("\n opt cycle:", count, "\n")
solver = opt_fnc(geom.coords, count)
count = count + 1
optimizer.send(solver)
etot_opt = solver[0]
grad_opt = solver[1]
relaxed = geom
#writing optimized coords to .xyz file
os.chdir(folder)
coordsname = open("opt_coords.xyz", "w")
from berny import Berny, optimize, geomlib
from berny.solvers import MopacSolver
from scr_old.gradient_plotter import log_berny_plotter
import numpy as np
import sys
# orig_stdout = sys.stdout
srm, smax = 0.05, 0.1
fxyz, logf, fopt = '/home/anastasiia/PycharmProjects/chem_structure/opted_mols/3-MnH2_opted.xyz',\
'3_opted'+str(srm)+'_stepmax_'+str(smax)+'.log', '3_opted_'+str(srm)+'_stepmax_'+str(smax)+'.xyz'
f = open(logf, 'w')
sys.stdout = f
optimizer = Berny(geomlib.readfile(fxyz),
steprms=srm,
stepmax=smax,
maxsteps=150)
final = optimize(optimizer, MopacSolver(cmd='/opt/mopac/run_script.sh'))
inertia_princpl = np.linalg.eigvalsh(final.inertia)
final.dump(open('3_berny_opt_mopac.xyz', 'w'), 'xyz')
# final.dump(open('TS-5-6_bopt.xyz', 'w'), 'xyz')
f.close()
log_berny_plotter(logf, title='3_berny_opt_mopac')
# for geom in optimizer:
# get energy and gradients for geom
# optimizer.send((energy, gradients))
def optimize(method, assert_convergence=ASSERT_CONV,
include_ghost=INCLUDE_GHOST, callback=None, **kwargs):
'''Optimize geometry with pyberny for the given method.
To adjust the convergence threshold, parameters can be set in kwargs as
below:
.. code-block:: python
conv_params = { # They are default settings
'gradientmax': 0.45e-3, # Eh/Angstrom
'gradientrms': 0.15e-3, # Eh/Angstrom
'stepmax': 1.8e-3, # Angstrom
'steprms': 1.2e-3, # Angstrom
}
from pyscf import geometric_solver
geometric_solver.optimize(method, **conv_params)
'''
t0 = time.clock(), time.time()
mol = method.mol.copy()
if 'log' in kwargs:
log = lib.logger.new_logger(method, kwargs['log'])
elif 'verbose' in kwargs:
log = lib.logger.new_logger(method, kwargs['verbose'])
else:
log = lib.logger.new_logger(method)
if isinstance(method, lib.GradScanner):
g_scanner = method
elif getattr(method, 'nuc_grad_method', None):
g_scanner = method.nuc_grad_method().as_scanner()
else:
raise NotImplementedError('Nuclear gradients of %s not available' % method)
if not include_ghost:
g_scanner.atmlst = numpy.where(method.mol.atom_charges() != 0)[0]
# temporary interface, taken from berny.py optimize function
berny_log = to_berny_log(log)
geom = to_berny_geom(mol, include_ghost)
optimizer = Berny(geom, log=berny_log, **kwargs)
t1 = t0
e_last = 0
for cycle, geom in enumerate(optimizer):
if log.verbose >= lib.logger.NOTE:
log.note('\nGeometry optimization cycle %d', cycle+1)
dump_mol_geometry(mol, geom.coords, log)
mol.set_geom_(_geom_to_atom(mol, geom, include_ghost), unit='Bohr')
energy, gradients = g_scanner(mol)
log.note('cycle %d: E = %.12g dE = %g norm(grad) = %g', cycle+1,
energy, energy - e_last, numpy.linalg.norm(gradients))
e_last = energy
if callable(callback):
callback(locals())
if assert_convergence and not g_scanner.converged:
raise RuntimeError('Nuclear gradients of %s not converged' % method)
optimizer.send((energy, gradients))
t1 = log.timer('geomoetry optimization cycle %d'%cycle, *t1)
t0 = log.timer('geomoetry optimization', *t0)
return mol
def test_optimize(mopac, test_case):
geom, n_ref = test_case()
berny = Berny(geom)
optimize(berny, mopac)
assert berny.converged
assert berny._n == n_ref
# Make wrapper functions for energy, force and dipole
def EnergyAndForce(molecule):
(Etotal, Ebp, Ebp_atom, Ecc, Evdw, mol_dipole, atom_charge,
gradient) = manager.EvalBPDirectEEUpdateSingle(molecule,
PARAMS["AN1_r_Rc"],
PARAMS["AN1_a_Rc"],
PARAMS["EECutoffOff"],
True)
energy = Etotal
return energy[0], (-1.0 * gradient[0] / JOULEPERHARTREE)
optimizer = Berny(geomlib.loads(xyz, 'xyz'),
maxsteps=1000,
gradientrms=0.0003,
gradientmax=0.003,
debug=True)
debug = []
last_geom = ""
for geom in optimizer:
molecule_xyz = geom.dumps('xyz')
molecule = Mol()
molecule.FromXYZString(molecule_xyz)
energy, gradients = EnergyAndForce(
molecule) # calculate energy and gradients of geom
info = optimizer.send((energy, gradients))
debug.append(info)
print('Final Geometry:')
print(geom.dumps('xyz'))
def TestBernyOpt():
from berny import Berny, geomlib
# a=MSet("kaggle_opt")
# a.Load()
# m=a.mols[8804]
# m = Mol()
# m.FromXYZString("""73
xyz = """73
O 3.11000 4.22490 -0.75810
O 4.72290 2.06780 -2.02160
O 3.28790 0.27660 -2.12830
O 7.57740 -2.18410 0.83530
O 6.93870 -0.24500 1.85400
N -0.44900 1.57680 0.54520
N 0.67240 -1.09000 0.16920
N -3.08650 0.73580 0.30880
N -2.08930 -2.17120 0.36140
C 3.15530 1.80910 -0.26920
C 1.94310 0.99350 0.14610
C 1.10470 3.11900 -0.07220
C 0.85730 1.76100 0.25120
C 2.53600 3.20940 -0.40610
C -0.01170 3.83890 -0.00490
C 1.80260 -0.45930 0.35870
C -0.97430 2.76340 0.37660
C 2.91740 -1.33270 0.77810
C 2.32400 -2.53760 0.79670
C 3.70160 1.28460 -1.55560
C 0.92000 -2.41280 0.43150
C -2.41080 3.07580 0.55540
C -0.29110 5.26060 -0.27150
C -3.30810 2.07470 0.53020
C -4.22430 -0.01890 0.37480
C -1.33840 -3.26350 -0.02560
C 0.02500 -3.41140 0.34800
C -4.76240 2.20220 0.74210
C -5.29980 0.95570 0.65430
C -3.38890 -2.29630 -0.08630
C -2.18770 -4.11130 -0.70980
C -3.46520 -3.50710 -0.75000
C 4.24800 -0.96910 1.13640
C -4.40070 -1.34110 0.20870
C 2.93270 -3.85050 1.16890
C -6.72700 0.53540 0.79750
C -1.82240 -5.42330 -1.29120
C -5.50430 3.40910 1.00050
C -4.63100 -4.03780 -1.35240
C 5.32530 -1.71620 0.83820
C 5.31710 1.65030 -3.25560
C -6.03270 4.16680 0.03880
C -5.68440 -3.34470 -1.89440
C 6.67040 -1.26750 1.24620
H 3.91490 1.82320 0.51520
H -2.69930 4.10740 0.71860
H -0.66660 5.75450 0.62990
H 0.61110 5.79090 -0.59250
H -1.03960 5.36580 -1.06280
H 0.35400 -4.43150 0.53040
H -5.40880 -1.73500 0.30730
H 4.36030 -0.04870 1.70090
H 3.88280 -3.75330 1.69880
H 2.27760 -4.40220 1.85250
H 3.09460 -4.46420 0.27690
H -6.83900 -0.17840 1.62010
H -7.08680 0.06850 -0.12540
H -7.38530 1.38280 1.01220
H -2.13640 -6.23380 -0.62560
H -2.30250 -5.57200 -2.26410
H -0.74330 -5.51440 -1.45110
H -5.62320 3.69670 2.04090
H -4.70070 -5.12240 -1.41710
H 5.25800 -2.63030 0.25800
H 4.57150 1.65850 -4.05620
H 5.75710 0.65460 -3.14550
H 6.11050 2.35890 -3.50730
H -6.58170 5.06770 0.29090
H -5.93330 3.91260 -1.01130
H -6.51300 -3.89300 -2.33170
H -5.71990 -2.26400 -1.94770
H 8.49250 -1.93230 1.08330
Mg -1.34673 0.02041 -0.06327"""
init_mol = Mol()
init_mol.FromXYZString(xyz)
# init_mol = a.mols[0]
net = UniversalNetwork(name="SF_Universal_master_jeherr_Thu_May_31_16.20.05_2018")
EF = net.GetEnergyForceRoutine(init_mol)
optimizer = Berny(
geomlib.loads(init_mol.__str__(), 'xyz'),
maxsteps=5000)
# gradientrms=0.0001,
# gradientmax=0.003,
# debug=True)
debug = []
last_geom = ""
init_mol.WriteXYZfile(fname="chlorophyll_berny")
for geom in optimizer:
molecule_xyz = geom.dumps('xyz')
molecule = Mol()
molecule.FromXYZString(molecule_xyz)
molecule.WriteXYZfile(fname="chlorophyll_berny")
energy, gradients = EF(molecule.coords) # calculate energy and gradients of geom
info = optimizer.send((energy, gradients))
debug.append(info)
print('Final Geometry:')
print(geom.dumps('xyz'))
def kernel(method, assert_convergence=ASSERT_CONV,
include_ghost=INCLUDE_GHOST, callback=None, **kwargs):
'''Optimize geometry with pyberny for the given method.
To adjust the convergence threshold, parameters can be set in kwargs as
below:
.. code-block:: python
conv_params = { # They are default settings
'gradientmax': 0.45e-3, # Eh/Angstrom
'gradientrms': 0.15e-3, # Eh/Angstrom
'stepmax': 1.8e-3, # Angstrom
'steprms': 1.2e-3, # Angstrom
}
from pyscf.geomopt import berny_solver
opt = berny_solver.GeometryOptimizer(method)
opt.params = conv_params
opt.kernel()
'''
t0 = time.clock(), time.time()
mol = method.mol.copy()
if 'log' in kwargs:
log = lib.logger.new_logger(method, kwargs['log'])
elif 'verbose' in kwargs:
log = lib.logger.new_logger(method, kwargs['verbose'])
else:
log = lib.logger.new_logger(method)
if isinstance(method, lib.GradScanner):
g_scanner = method
elif getattr(method, 'nuc_grad_method', None):
g_scanner = method.nuc_grad_method().as_scanner()
else:
raise NotImplementedError('Nuclear gradients of %s not available' % method)
if not include_ghost:
g_scanner.atmlst = numpy.where(method.mol.atom_charges() != 0)[0]
# When symmetry is enabled, the molecule may be shifted or rotated to make
# the z-axis be the main axis. The transformation can cause inconsistency
# between the optimization steps. The transformation is muted by setting
# an explict point group to the keyword mol.symmetry (see symmetry
# detection code in Mole.build function).
if mol.symmetry:
mol.symmetry = mol.topgroup
# temporary interface, taken from berny.py optimize function
berny_log = to_berny_log(log)
geom = to_berny_geom(mol, include_ghost)
optimizer = Berny(geom, log=berny_log, **kwargs)
t1 = t0
e_last = 0
for cycle, geom in enumerate(optimizer):
if log.verbose >= lib.logger.NOTE:
log.note('\nGeometry optimization cycle %d', cycle+1)
dump_mol_geometry(mol, geom.coords, log)
if mol.symmetry:
geom.coords = symmetrize(mol, geom.coords)
mol.set_geom_(_geom_to_atom(mol, geom, include_ghost), unit='Bohr')
energy, gradients = g_scanner(mol)
log.note('cycle %d: E = %.12g dE = %g norm(grad) = %g', cycle+1,
energy, energy - e_last, numpy.linalg.norm(gradients))
e_last = energy
if callable(callback):
callback(locals())
if assert_convergence and not g_scanner.converged:
raise RuntimeError('Nuclear gradients of %s not converged' % method)
optimizer.send((energy, gradients))
t1 = log.timer('geomoetry optimization cycle %d'%cycle, *t1)
t0 = log.timer('geomoetry optimization', *t0)
return optimizer._converged, mol
def optimize(self):
fout_xyz = open(self._geomopt['fname_gopt_xyz'], 'w', 1)
fout_log = open(self._geomopt['fname_gopt_log'], 'w', 1)
optimizer = Berny(self._qm_geom)
qm_natom = len(self._qm_geom)
def step_func(x):
if x < -0.5:
x = -0.5
elif x > 0.5:
x = 0.5
return x
qm_crds_old = self._qm_geom.coords
prt_crds = self._prt_geom.coords
ener_last = 0.0
qm_grd_norm_last = 0.0
ener_QM0 = 0.0
for cycle, qm_geom in enumerate(optimizer):
qm_crds_new = qm_geom.coords
d_crds = qm_crds_new - qm_crds_old
for atmId in self._qm2mm_index:
resId, atomName = atmId.split(':')
if resId not in ['LIG1']:
mm_idx = self._qm2mm_index[atmId]
qm_idx = self._qmatm_index[atmId]
if atomName not in ['CA']:
prt_crds[mm_idx] = qm_crds_new[qm_idx]
ener_QMMM, ener_const, grds_QM, esp_QM, \
ener_QMMM_vdw, ener_PRT, grds_PRT = self.pot_grad(
qm_geom, prt_crds)
if cycle == 0:
ener_QM0 = ener_QMMM
ener_QMMM -= ener_QM0
ener = ener_QMMM + ener_const + ener_QMMM_vdw + ener_PRT
qm_grd_norm = np.linalg.norm(grds_QM)
print(' %5d' % qm_natom, file=fout_xyz)
print('cycle %3d: E = %12.6f %12.6f %10.4f %10.4f %10.4f %12.6f' %
(cycle + 1, ener, ener_QMMM, ener_const, ener_QMMM_vdw,
ener_PRT, ener_QM0),
file=fout_xyz)
print(
'cycle %3d: E = %12.6f %12.6f %10.4f %10.4f %10.4f dE = %.6g norm(grad) = %g'
% (cycle + 1, ener, ener_QMMM, ener_const, ener_QMMM_vdw,
ener_PRT, ener - ener_last, qm_grd_norm),
file=fout_log)
for i in range(qm_natom):
print('%4s %10.6f %10.6f %10.6f' %
(self._qm_geom.species[i], qm_crds_new[i, 0],
qm_crds_new[i, 1], qm_crds_new[i, 2]),
file=fout_xyz)
print('%5d %4s %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f' %
((i + 1), self._qm_geom.species[i], d_crds[i, 0],
d_crds[i, 1], d_crds[i, 2], grds_QM[i, 0],
grds_QM[i, 1], grds_QM[i, 2]),
file=fout_log)
if (cycle + 1) % 2 == 0:
self.save_coordinates(qm_crds_new, prt_crds)
dE = ener - ener_last
if abs(dE) / qm_natom < 1.0e-8:
break
dG = qm_grd_norm - qm_grd_norm_last
if abs(dG) / qm_natom < 1.0e-8:
break
ener_last = ener
qm_grd_norm_last = qm_grd_norm
qm_crds_old = qm_crds_new
for atmId in self._qm2mm_index:
resId, atomName = atmId.split(':')
if resId[:3] not in ['LIG'] and atomName not in ['CA']:
'''
'CA' belongs to MM
Except 'CA', bond, angle, and torsional gradients, which are estimated within MM, are copied to QM particles.
'''
mm_idx = self._qm2mm_index[atmId]
qm_idx = self._qmatm_index[atmId]
grds_QM[qm_idx] += grds_PRT[mm_idx]
grds_PRT[mm_idx, 0] = 0
grds_PRT[mm_idx, 1] = 0
grds_PRT[mm_idx, 2] = 0
grds_PRT = np.array([[step_func(x),
step_func(y),
step_func(z)] for x, y, z in grds_PRT])
prt_crds -= 0.01 * grds_PRT
grds_QM = np.array([[step_func(x),
step_func(y),
step_func(z)] for x, y, z in grds_QM])
optimizer.send((ener, grds_QM))
self.save_coordinates(qm_crds_old, prt_crds)