def test_pyscf():
from pyscf import gto, dft
from pyscf.geomopt.berny_solver import as_berny_solver
mf = dft.RKS(gto.M(atom=list(ethanol), basis='3-21g', verbose=0))
mf.xc = 'pbe'
solver = as_berny_solver(mf)
final = optimize(solver, ethanol)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([15.39, 54.38, 63.30], rel=1e-3)
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)
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 test_optimize(mopac, test_case):
geom, n_ref = test_case()
berny = Berny(geom)
optimize(berny, mopac)
assert berny.converged
assert berny._n == n_ref
def test_aniline():
solver = MopacSolver()
final = optimize(solver, aniline, steprms=0.01, stepmax=0.05, maxsteps=8)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([90.94, 193.1, 283.9], rel=1e-3)
def test_ethanol():
solver = MopacSolver()
final = optimize(solver, ethanol, steprms=0.01, stepmax=0.05, maxsteps=5)
inertia_princpl = np.linalg.eigvalsh(final.inertia)
assert inertia_princpl == approx([14.95, 52.58, 61.10], rel=1e-3)