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 cyanogen():
return geomlib.readfile(resource_filename('tests', 'cyanogen.xyz'))
def aniline():
return geomlib.readfile(resource_filename('tests', 'aniline.xyz'))
def ethanol():
return geomlib.readfile(resource_filename('tests', 'ethanol.xyz'))
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 water():
return geomlib.readfile(resource_filename('tests', 'water.xyz')), 7
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")