Grouping tests for NAMD

[amruthesht]

imdclient/imdclient/tests/test_namd.py

Lines 107 to 127 in 9e906f0

	# Since NAMD does not write velocities, forces to the DCD file, we need to do so seperately by extracting that info from theri respective DCD files
	# Compare velocities
	def test_compare_imd_to_true_traj_vel(self, imd_u, true_u_vel, first_frame):
	for i in range(first_frame, len(true_u_vel.trajectory)):
	assert_allclose_with_logging(
	# Unit conversion
	true_u_vel.trajectory[i].positions * 20.45482706,
	imd_u.trajectory[i - first_frame].velocities,
	atol=1e-03,
	)
	# Compare forces
	def test_compare_imd_to_true_traj_forces(
	self, imd_u, true_u_force, first_frame
	):
	for i in range(first_frame, len(true_u_force.trajectory)):
	assert_allclose_with_logging(
	true_u_force.trajectory[i].positions,
	imd_u.trajectory[i - first_frame].forces,
	atol=1e-03,
	)

Currently, due to NAMD's inherent output scheme (writing positions, velocities and force information to separate files), the tests for each have been dealt with separately by creating universes for each as highlighted in the code above.

A better and cleaner alternative would be read all the information into a single universe by reading information for all 3 files. The most efficient way to do this needs to be figured out. The most naive approach would be to create 3 separate universes and copy relevant data from two of them into the third.

[hmacdope]

@yuxuanzhuang would you be able to help out here?

[yuxuanzhuang]

I don't think there's a simple way to merge all three DCD files into one universe so creating three universes makes sense to me.

If you want to have one unified universe with all the information, you can create a universe with all the data moved into memory

u = mda.Universe(
            (tmp_path / topol),
            (tmp_path / "alanin.dcd"), in_memory=True)

u_vel = mda.Universe(
            (tmp_path / topol),
            (tmp_path / "alanin.vel.dcd"), in_memory=True)

u_force = mda.Universe(
            (tmp_path / topol),
            (tmp_path / "alanin.force.dcd"), in_memory=True)

u.trajectory.velocity_array = u_vel.trajectory.coordinate_array * 20.45482706
u.trajectory.force_array = u_force.trajectory.coordinate_array

yield u
...

[amruthesht]

If the best approach possible right now is to just create 3 separate universes, I'll go ahead and implement that, thank you!

[ljwoods2]

Closed by #54 which uses 3 universe approach