def test_optimize(tmpdir):
tmpdir.chdir()
be = Molecule(name="Be", atoms=[('Be', )], charge=0, multiplicity=1)
template = '''***,be ccpvdz tight fs test
memory,100,m
%geometry
%basis
%core
{rhf; wf,4,1,0}
cisd
'''
mp = Molpro(exevar="MOLPRO_EXE", runopts=["-s", "-n", "1", "-d", "."])
corefs = {'Be': [('s', 'exp', 1, (1.1, )), ('p', 'exp', 1, (4.2, ))]}
ccpvdz_str = '''basis={
!BAZA Petersona
s,Be,2.940000E+03,4.412000E+02,1.005000E+02,2.843000E+01,9.169000E+00,3.196000E+00,1.159000E+00,1.811000E-01,5.890000E-02;
c,1.9,6.800000E-04,5.236000E-03,2.660600E-02,9.999300E-02,2.697020E-01,4.514690E-01,2.950740E-01,1.258700E-02,-3.756000E-03;
c,1.9,-1.230000E-04,-9.660000E-04,-4.831000E-03,-1.931400E-02,-5.328000E-02,-1.207230E-01,-1.334350E-01,5.307670E-01,5.801170E-01;
c,9.9,1.000000E+00;
p,Be,3.619000E+00,7.110000E-01,1.951000E-01,6.018000E-02;
c,1.4,2.911100E-02,1.693650E-01,5.134580E-01,4.793380E-01;
c,4.4,1.000000E+00;
!
!d,Be,2.354000E-01;
!c,1.1,1.000000E+00;
}
'''
ccpvdz = BasisSet.from_str(ccpvdz_str, fmt='molpro')
bso = BSOptimizer(objective='cisd total energy',
core=[[1, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0,
0]],
template=template,
verbose=True,
code=mp,
mol=be,
fsopt=corefs,
staticbs={'Be': ccpvdz},
uselogs=True,
runcore=True,
fname='be_tight.inp')
bso.run()
coreenergy = -0.031510764610001019
assert abs(bso.result.fun - coreenergy) < 1.0e-8, 'wrong objective'
def test_to_json():
bs = BasisSet.from_str(VTZGAUSSIAN, fmt='gaussian', name='VTZ')
bsdumped = bs.to_json(indent=4)
bsloaded = BasisSet.from_json(bsdumped)
assert bs.name == bsloaded.name, 'inconsistent name'
assert bs.element == bsloaded.element, 'inconsistent element'
for shell, funs in bs.functions.items():
assert shell in bsloaded.functions.keys(), 'missing shell {}'.format(shell)
assert np.allclose(funs['e'], bsloaded.functions[shell]['e'])
for f1, f2 in zip(funs['cf'], bsloaded.functions[shell]['cf']):
assert np.allclose(f1['idx'], f2['idx']), 'inconsistent idx'
assert np.allclose(f1['cc'], f2['cc']), 'inconsistent cc'
def test_optimize(tmpdir):
tmpdir.chdir()
dalton = Dalton(exevar='DALTON_EXE',
runopts=['-nobackup', '-noarch', '-d'])
beh = Molecule(name="BeH-", atoms=[('Be',), ('H', (0.0, 0.0, 2.724985))],
sym="cnv 2", charge=-1, multiplicity=1)
moltemplate = '''INTGRL
basis set optimization
test dalton calculator
Atomtypes=2 Charge=-1 Integrals=1.0D-20
%basis
'''
hftemplate = '''**DALTON INPUT
.RUN WAVE FUNCTIONS
**WAVE FUNCTION
.HF
**END OF DALTON INPUT
'''
fname = {'dal': 'hf.dal', 'mol': 'BeH-.mol'}
template = {'mol': moltemplate, 'dal': hftemplate}
optimization = {"method": "Nelder-Mead",
"tol": 1.0e-4,
"options": {"maxiter": 100,
"disp": True}
}
ccpvdz_str = '''basis={
s,Be,2.940000E+03,4.412000E+02,1.005000E+02,2.843000E+01,9.169000E+00,3.196000E+00,1.159000E+00,1.811000E-01,5.890000E-02;
c,1.9,6.800000E-04,5.236000E-03,2.660600E-02,9.999300E-02,2.697020E-01,4.514690E-01,2.950740E-01,1.258700E-02,-3.756000E-03;
c,1.9,-1.230000E-04,-9.660000E-04,-4.831000E-03,-1.931400E-02,-5.328000E-02,-1.207230E-01,-1.334350E-01,5.307670E-01,5.801170E-01;
c,9.9,1.000000E+00;
p,Be,3.619000E+00,7.110000E-01,1.951000E-01,6.018000E-02;
c,1.4,2.911100E-02,1.693650E-01,5.134580E-01,4.793380E-01;
c,4.4,1.000000E+00;
d,Be,2.354000E-01;
c,1.1,1.000000E+00;
s, H , 13.0100000, 1.9620000, 0.4446000, 0.1220000, 0.0297400
c, 1.3, 0.0196850, 0.1379770, 0.4781480
c, 4.4, 1
c, 5.5, 1
p, H , 0.7270000, 0.1410000
c, 1.1, 1
c, 2.2, 1
}
'''
ccpvdz = BasisSet.from_str(ccpvdz_str, fmt='molpro')
augfs = {'Be': [('s', 'exp', 1, (0.02,)),
('p', 'exp', 1, (0.01,)),
('d', 'exp', 1, (0.07,))]}
bso = BSOptimizer(objective='hf total energy', template=template,
code=dalton, mol=beh,
fsopt=augfs, staticbs=ccpvdz, verbose=True,
optalg=optimization, fname=fname)
bso.run()
energy = -15.131589405116999
assert abs(bso.result.fun - energy) < 1.0e-8, 'wrong objective'
def test_optimize(tmpdir):
tmpdir.chdir()
psi = Psi4(exevar="PSI4_EXE", runopts=["-n", "4"])
beh = Molecule(name="BeH-",
atoms=[('Be', ), ('H', (0.0, 0.0, 2.724985))],
sym="cnv 2",
charge=-1,
multiplicity=1)
psitemp = '''#! test BeH-
memory 100 mb
molecule beh {
Be 0.0000 0.0000 0.0000
H 0.0000 0.0000 1.4420
units angstrom
}
beh.set_molecular_charge(-1)
beh.set_multiplicity(1)
basis = {
assign mybasis
[ mybasis ]
spherical
%basisset
}
set {
freeze_core True
e_convergence 13
d_convergence 10
}
energy('cisd')
'''
optimization = {
"method": "Nelder-Mead",
"tol": 1.0e-4,
"options": {
"maxiter": 100,
"disp": True,
}
}
ccpvdz_str = '''basis={
s,Be,2.940000E+03,4.412000E+02,1.005000E+02,2.843000E+01,9.169000E+00,3.196000E+00,1.159000E+00,1.811000E-01,5.890000E-02;
c,1.9,6.800000E-04,5.236000E-03,2.660600E-02,9.999300E-02,2.697020E-01,4.514690E-01,2.950740E-01,1.258700E-02,-3.756000E-03;
c,1.9,-1.230000E-04,-9.660000E-04,-4.831000E-03,-1.931400E-02,-5.328000E-02,-1.207230E-01,-1.334350E-01,5.307670E-01,5.801170E-01;
c,9.9,1.000000E+00;
p,Be,3.619000E+00,7.110000E-01,1.951000E-01,6.018000E-02;
c,1.4,2.911100E-02,1.693650E-01,5.134580E-01,4.793380E-01;
c,4.4,1.000000E+00;
d,Be,2.354000E-01;
c,1.1,1.000000E+00;
s, H , 13.0100000, 1.9620000, 0.4446000, 0.1220000, 0.0297400
c, 1.3, 0.0196850, 0.1379770, 0.4781480
c, 4.4, 1
c, 5.5, 1
p, H , 0.7270000, 0.1410000
c, 1.1, 1
c, 2.2, 1
}
'''
ccpvdz = BasisSet.from_str(ccpvdz_str, fmt='molpro')
augfs = {
'Be': [('s', 'exp', 1, (0.02, )), ('p', 'exp', 1, (0.01, )),
('d', 'exp', 1, (0.07, ))]
}
bso = BSOptimizer(objective='cisd total energy',
template=psitemp,
code=psi,
mol=beh,
fsopt=augfs,
staticbs=ccpvdz,
core=[1, 0, 0, 0, 0, 0, 0, 0],
verbose=True,
optalg=optimization,
fname='beh_aug.dat')
bso.run()
energy = -15.204232302468
assert abs(bso.result.fun - energy) < 1.0e-8, 'wrong objective'
def test_optimize(tmpdir):
tmpdir.chdir()
gamesstemp = ''' $CONTRL
scftyp=rhf
cityp=guga
runtyp=energy
maxit=30
mult=1
ispher=1
units=bohr
exetyp=run
$END
$SYSTEM
timlim=525600
mwords=100
$END
$CIDRT
iexcit=2
nfzc=2
ndoc=2
nval=40
group=d2h
$END
%basis
'''
be2X = Molecule(name="Be2",
atoms=[('Be', (0.0, 0.0, -1.5)),
('H', (0.0, 0.0, 0.0), True),
('Be', (0.0, 0.0, 1.5))],
sym="dnh 2",
charge=0,
multiplicity=1,
unique=[0, 1])
bsstr = '''basis={
s,Be,2.940000E+03,4.412000E+02,1.005000E+02,2.843000E+01,9.169000E+00,3.196000E+00,1.159000E+00,1.811000E-01,5.890000E-02;
c,1.9,6.800000E-04,5.236000E-03,2.660600E-02,9.999300E-02,2.697020E-01,4.514690E-01,2.950740E-01,1.258700E-02,-3.756000E-03;
c,1.9,-1.230000E-04,-9.660000E-04,-4.831000E-03,-1.931400E-02,-5.328000E-02,-1.207230E-01,-1.334350E-01,5.307670E-01,5.801170E-01;
c,9.9,1.000000E+00;
p,Be,3.619000E+00,7.110000E-01,1.951000E-01,6.018000E-02;
c,1.4,2.911100E-02,1.693650E-01,5.134580E-01,4.793380E-01;
c,4.4,1.000000E+00;
d,Be,2.354000E-01;
c,1.1,1.000000E+00;
}
'''
vdz = BasisSet.from_str(bsstr, fmt='molpro')
optimization = {
"method": "CG",
"tol": 1.0e-4,
"jacob": False,
"options": {
"maxiter": 100,
"disp": True,
'eps': 1.0e-3
}
}
gams = GamessUS(exevar="GAMESS_EXE", runopts=['1'])
midbond = {'H': [('s', 'et', 4, (0.05, 2.0)), ('p', 'et', 4, (0.04, 2.0))]}
bso = BSOptimizer(objective='cisd total energy',
template=gamesstemp,
code=gams,
mol=be2X,
fsopt=midbond,
staticbs={'Be': vdz},
core=2,
fname='midbond.inp',
verbose=True,
optalg=optimization)
bso.run()
energy = -29.1326831928
assert abs(bso.result.fun - energy) < 1.0e-8, 'wrong objective'
