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35 """Test gmxapi._gmxapi file I/O routines."""
41 import gmxapi.simulation.fileio
42 from gmxapi import _gmxapi
45 @pytest.mark.usefixtures('cleandir')
46 def test_core_read_tpr(spc_water_box):
47 tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
48 parameters: _gmxapi.SimulationParameters = tpr_filehandle.params()
49 assert 'nsteps' in parameters.extract()
50 assert 'foo' not in parameters.extract()
51 assert parameters.extract()['nsteps'] == 2
54 @pytest.mark.usefixtures('cleandir')
55 def test_core_rewrite_tprfile(spc_water_box):
56 """Test _gmxapi.rewrite_tprfile for update of end_time.
58 Set a new end time that is 5000 steps later than the original. Read dt
59 from file to avoid floating point round-off errors.
61 Transitively test gmx.fileio.read_tpr()
63 tpr_filename = spc_water_box
64 additional_steps = 5000
65 tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
66 params = tpr_filehandle.params().extract()
68 nsteps = params['nsteps']
69 init_step = params['init-step']
70 initial_endtime = (init_step + nsteps) * dt
71 new_endtime = initial_endtime + additional_steps * dt
72 _, temp_filename = tempfile.mkstemp(suffix='.tpr')
73 _gmxapi.rewrite_tprfile(source=tpr_filename, destination=temp_filename, end_time=new_endtime)
74 tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
76 params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
78 nsteps = params['nsteps']
79 init_step = params['init-step']
80 assert (init_step + nsteps) * dt == new_endtime
82 os.unlink(temp_filename)
85 @pytest.mark.usefixtures('cleandir')
86 def test_core_read_and_write_tpr_file(spc_water_box):
87 """Test gmx.fileio.write_tpr_file() using gmx.core API.
89 additional_steps = 5000
91 tpr_filehandle: _gmxapi.TprFile = _gmxapi.read_tprfile(os.fsencode(spc_water_box))
92 sim_input: _gmxapi.SimulationParameters = tpr_filehandle.params()
93 params: dict = sim_input.extract()
94 nsteps = params['nsteps']
95 init_step = params['init-step']
97 # Choose a new nsteps to check integer parameter setting.
98 new_nsteps = init_step + additional_steps
99 # Choose a new dt to check floating point parameter setting
100 new_dt = params['dt'] * 2.
102 sim_input.set('nsteps', new_nsteps)
103 sim_input.set('dt', new_dt)
105 _, temp_filename = tempfile.mkstemp(suffix='.tpr')
106 _gmxapi.write_tprfile(temp_filename, sim_input)
108 tprfile = gmxapi.simulation.fileio.TprFile(temp_filename, 'r')
110 params = gmxapi.simulation.fileio.read_tpr(fh).parameters.extract()
111 # Note that we have chosen an exactly representable dt for spc_water_box.
112 # Otherwise, we would have to use pytest.approx with a suitable tolerance.
113 assert params['dt'] == new_dt
114 assert params['nsteps'] != nsteps
115 assert params['nsteps'] == new_nsteps
117 os.unlink(temp_filename)