calculator = Pyscf(method='hf', label="ase", atoms=atoms)
calculator.run_qr(atoms,
coordinates=None,
charge=None,
pointcharges=None,
command=None,
define_str=None)
assert approx_equal(calculator.energy_free, -24894.129755)
assert approx_equal(calculator.forces.tolist(),
[[10.3539855, -109.02533792, -52.22553528],
[-89.1104867, 135.541275, -63.22351153],
[81.34525894, -32.53859855, 36.0316453],
[17.81046893, 0.39223847, 28.47319708],
[-20.39922667, 5.630423, 50.94420443]])
if (__name__ == "__main__"):
pyscf_installed = False
try:
import pyscf
from pyscf import gto, scf, grad, dft
pyscf_installed = True
except ImportError:
#"Pyscf not installed. Please run: qrefine.python pip -m install pyscf"
pass
prefix = os.path.basename(__file__).replace(".py", "")
run_tests.runner(function=run, prefix=prefix, disable=not pyscf_installed)
TER
'''
def run(prefix):
fn = 'expansion.pdb'
f = open(fn, 'w')
f.write(expansion)
f.close()
fn = 'test_alt_loc_original.pdb'
f = open(fn, 'w')
f.write(pdb_lines)
f.close()
cmd = 'phenix.python %s/completion.py %s model_completion=False original_pdb_filename=expansion.pdb' % (
qrefine_path, fn)
if 0: print(cmd)
easy_run.go(cmd)
fnc = '%s_capping.pdb' % fn.replace('.pdb', '')
cmd = 'phenix.pdb_interpretation %s' % fnc
if 0: print(cmd)
rc = easy_run.go(cmd)
assert ' H 47 1.00' in rc.stdout_lines
os.remove(fn)
os.remove(fnc)
return rc
if (__name__ == '__main__'):
prefix = os.path.basename(__file__).replace(".py", "")
run_tests.runner(function=run, prefix=prefix, disable=False)
calculatorANIccx = TorchAni(method='ani-1ccx', label="ase", atoms=atoms)
calculatorANIccx.run_qr(atoms=atoms,
coordinates=atoms.get_positions(),
charge=0,
pointcharges=None)
assert calculatorANIccx.method == 'ani-1ccx'
assert approx_equal(calculatorANIccx.energy_free, -40.4256210327)
assert approx_equal(calculatorANIccx.forces,
[[0.0312, -0.1272, -0.0511],
[-0.1200, 0.1628, -0.0761], [0.0856, -0.0448, 0.0407],
[0.0219, 0.0044, 0.0343], [-0.0187, 0.0049, 0.0521]],
0.001)
if (__name__ == "__main__"):
torchani_installed = False
try:
import torch
device = torch.device('cpu')
import torchnani
from qrefine.plugin.ase.torchani_qr import TorchAni
torchani_installed = True
except ImportError:
pass
prefix = os.path.basename(__file__).replace(".py", "")
run_tests.runner(function=run,
prefix=prefix,
disable=not torchani_installed)
[3.224648029245346, 17.928547580646576, -4.524288383451061],
[-14.150630324115214, 1.2147768632076443, 1.967302103238517],
[-11.589212064363652, -6.444221705381739, -4.77406901682601],
[-5.5705251392947135, -49.58353381805122, 17.851453490207053],
[12.42994083133531, -31.32628534955386, 0.5620932081847977],
[-15.209140041336132, 2.6841055262949185, 18.113311015189275],
[-38.73187194009035, -15.72274317196305, -11.82050674146153],
[36.242545183467506, -10.805354680557413, -12.277902260267444],
[15.232739148782514, -4.663316010381281, 8.999606560034826],
[59.63334514038209, 26.088864339029772, 11.30765051583584],
[15.608156356402093, 27.943937629842292, -43.96675247210592],
[18.13331849770548, 7.431414655697998, 16.906001192291857],
[17.86199385016078, -8.699557589383213, 33.00195465513993],
[-10.848074631757044, 39.029932538400196, -25.227204796906726],
[-39.85554941979901, 1.527429754721101, -19.432085940661143],
[31.92966974414988, -30.73366946479253, -4.944928236082764],
[3.6813964573627045, -4.724979244557905, -38.6569203686534],
[14.529074495458673, 6.242069503845828, 12.534003126275708]], 0.001)
if(__name__ == "__main__"):
tensormol_installed = False
try:
import TensorMol
from qrefine.plugin.ase.tensormol_qr import TensormolCalculator
tensormol_installed = True
except ImportError:
pass
prefix = os.path.basename(__file__).replace(".py","")
run_tests.runner(function=run, prefix=prefix, disable=not tensormol_installed)
