amber test fails
Test with --calculators=amber invariably failed. It seems that the file "2h2o.pdb" referred to in the test is not provided or not found. Adding the following to the beginning of ~/.local/lib/python2.7/site-packages/ase/test/amber/amber.py solved the problem:
with open('2h2o.pdb', 'w') as outfile: outfile.write("""\ ATOM 1 O HOH 1 0.000 0.000 0.000 1.00 0.00 O ATOM 3 H1 HOH 1 -0.241 -0.971 0.000 1.00 0.00 H ATOM 6 H2 HOH 1 1.050 0.100 0.100 1.00 0.00 H TER ATOM 2 O HOH 2 2.200 0.000 0.000 1.00 0.00 O ATOM 4 H2 HOH 2 2.459 0.966 0.000 1.00 0.00 H ATOM 5 H1 HOH 2 2.459 -0.483 0.837 1.00 0.00 H END """)
However, with --calculators=amber activated, test of calculator/traj.py failed (output below). It seems, that test is now trying to use amber (without providing the required input files).
====================================================================== ERROR: calculator/traj.py
Traceback (most recent call last): File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/test/init.py", line 51, in testfile exec(compile(fd.read(), self.filename, 'exec'), {}) File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/test/calculator/traj.py", line 38, in h2(name, par) File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/test/calculator/traj.py", line 13, in h2 e = h2.get_potential_energy() File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/atoms.py", line 682, in get_potential_energy energy = self._calc.get_potential_energy(self) File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/calculators/calculator.py", line 422, in get_potential_energy energy = self.get_property('energy', atoms) File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/calculators/calculator.py", line 461, in get_property self.calculate(atoms, [name], system_changes) File "/homeappl/home/henschel/.local/lib/python2.7/site-packages/ase/calculators/calculator.py", line 620, in calculate (self.name, errorcode)) RuntimeError: amber returned an error: 1