def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
with path('quickff.data.systems.uio66-zr-brick', 'system.chk') as fn:
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir('test_methane_%s'%('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,fn_sys=fn_sys,do_cross_DSS=True,do_cross_DSD=True,
do_cross_DAA=True,do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program,equal=consistent)
def test_methane_consistent_crossterms():
with log.section('NOSETEST', 2):
system, ai = read_system('methane/gaussian.fchk')
set_ffatypes(system, 'high')
for consistent in [False, True]:
with tmpdir('test_methane_%s'%('consistent' if consistent else 'inconsistent')) as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=consistent,
fn_yaff=fn_yaff,fn_sys=fn_sys,do_cross_DSS=True,do_cross_DSD=True,
do_cross_DAA=True,do_cross_DAD=True))
program.run()
compare_crossterm_rest_values(program,equal=consistent)
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print line
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 2
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert f.next() == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in xrange(natom+1):
f.next()
line = f.next()
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nbond*2
f.next()
line = f.next()
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == ntheta*3
f.next()
line = f.next()
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([f.next() for iline in xrange(nline)])).split()
assert len(numbers) == nphi*4
f.next()
line = f.next()
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0
def test_output_charmm22():
with log.section('NOSETST', 2):
system, ai = read_system('ethanol/gaussian.fchk')
set_ffatypes(system, 'low')
with tmpdir('test_output_charmm22') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_charmm22_prm = os.path.join(dn, 'test.prm')
fn_charmm22_psf = os.path.join(dn, 'test.psf')
fn_sys = os.path.join(dn, 'system.chk')
settings = Settings(
do_cross_ASS=False, do_cross_ASA=False,
fn_yaff=fn_yaff, fn_sys=fn_sys,
fn_charmm22_prm=fn_charmm22_prm,
fn_charmm22_psf=fn_charmm22_psf,
)
program = DeriveFF(system, ai, settings)
program.run()
assert os.path.isfile(fn_yaff)
assert os.path.isfile(fn_charmm22_prm)
assert os.path.isfile(fn_charmm22_psf)
assert os.path.isfile(fn_sys)
# Count the number of BOND, ANGLES and DIHEDRAL lines in the PRM file.
counts = {}
with open(fn_charmm22_prm, 'r') as f:
for line in f:
print(line)
line = line[:line.find('!')].strip()
if len(line) == 0:
continue
if line in ['BONDS','ANGLES', 'DIHEDRALS', 'IMPROPER']:
key = line
counts[key] = 0
else:
counts[key] += 1
assert counts['BONDS'] == 4
assert counts['ANGLES'] == 5
assert counts['DIHEDRALS'] == 3
assert counts['IMPROPER'] == 0
# Count the number atoms, bonds, angles and dihedrals in the PSF file and
# check for consistency.
with open(fn_charmm22_psf, 'r') as f:
natom = 0
assert next(f) == 'PSF\n'
for line in f:
if '!NATOM' in line:
natom = int(line.split()[0])
break
assert natom == system.natom
for iatom in range(natom+1):
next(f)
line = next(f)
assert '!NBOND: bonds' in line
nbond = int(line.split()[0])
nline = int(np.ceil(nbond/4.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nbond*2
next(f)
line = next(f)
assert '!NTHETA: angles' in line
ntheta = int(line.split()[0])
nline = int(np.ceil(ntheta/3.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == ntheta*3
next(f)
line = next(f)
assert '!NPHI: dihedrals' in line
nphi = int(line.split()[0])
nline = int(np.ceil(nphi/2.0))
numbers = (''.join([next(f) for iline in range(nline)])).split()
assert len(numbers) == nphi*4
next(f)
line = next(f)
assert '!NIMPHI: impropers' in line
nimphi = int(line.split()[0])
assert nimphi == 0