imdclient 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

imdclient/tests/test_manual.py

@@ -1,14 +1,11 @@
+import imdclient
 from imdclient.IMD import IMDReader
-import pytest
 import MDAnalysis as mda
-from MDAnalysisTests.coordinates.base import assert_timestep_almost_equal
-from numpy.testing import (
-    assert_allclose,
-)
+from numpy.testing import assert_allclose
 import numpy as np
-from .base import assert_allclose_with_logging
 from pathlib import Path
-
+import time
+import argparse
 import logging
 
 logger = logging.getLogger("imdclient.IMDClient")
@@ -20,74 +17,233 @@ file_handler.setFormatter(formatter)
 logger.addHandler(file_handler)
 logger.setLevel(logging.DEBUG)
 
+"""
+Tool for running IMDv3 integration tests via the command line.
 
-class TestIMDv3Manual:
-    """
-    Tool for running IMDv3 integration tests via the command line.
+To use, start the simulation, wait for it to be ready for an IMD connection,
+and then run this command relative to the root of the cloned respository:
 
-    To use, start the simulation, wait for it to be ready for an IMD connection,
-    and then run this command relative to the root of the cloned respository:
+python imdclient/tests/test_manual.py \
+    --topol_path <path/to/topology> \
+    --traj_path <path/to/trajectory> \
+    --first_frame <first frame to compare> \
+    --tmp_path <temporary directory for IMD trajectory>
 
-    pytest -s imdclient/tests/test_manual.py \
-        --topol_path_arg <path/to/topology> \
-        --traj_path_arg <path/to/trajectory> \
-        --first_frame_arg <first traj frame to compare to IMD>
+Where the topology is the same topology as the IMD system, the trajectory is the path where
+the trajectory of the running simulation is being written, and the first frame is the first frame of the
+trajectory which should be compared to IMD data read from the socket (0 for GROMACS and NAMD, 1 for LAMMPS)
+"""
+
+
+def assert_allclose_with_logging(a, b, rtol=1e-07, atol=0, equal_nan=False):
+    """
+    Custom function to compare two arrays element-wise, similar to np.testing.assert_allclose,
+    but logs all non-matching values.
 
-    Where the topology is the same topology as the IMD system, the trajectory is the path where
-    the trajectory of the running simulation is being written, and the first frame is the first frame of the
-    trajectory which should be compared to IMD data read from the socket (0 for GROMACS and NAMD, 1 for LAMMPS)
+    Parameters:
+    a, b : array_like
+        Input arrays to compare.
+    rtol : float
+        Relative tolerance.
+    atol : float
+        Absolute tolerance.
+    equal_nan : bool
+        Whether to compare NaNs as equal.
     """
+    # Convert inputs to numpy arrays
+    a = np.asarray(a)
+    b = np.asarray(b)
+
+    # Compute the absolute difference
+    diff = np.abs(a - b)
+
+    # Check if values are within tolerance
+    not_close = diff > (atol + rtol * np.abs(b))
+
+    # Check if there are any NaNs and handle them if necessary
+    if equal_nan:
+        nan_mask = np.isnan(a) & np.isnan(b)
+        not_close &= ~nan_mask
+
+    # Log all the values that are not close
+    if np.any(not_close):
+        print("The following values do not match within tolerance:")
+        for idx in np.argwhere(not_close):
+            logger.debug(
+                f"a[{tuple(idx)}]: {a[tuple(idx)]}, b[{tuple(idx)}]: {b[tuple(idx)]}, diff: {diff[tuple(idx)]}"
+            )
+        # Optionally raise an error after logging if you want it to behave like assert
+        raise AssertionError("Arrays are not almost equal.")
+    else:
+        print("All values are within tolerance.")
+
 
-    @pytest.fixture()
-    def true_u(self, imd_u, topol_path_arg, traj_path_arg):
-        return mda.Universe(topol_path_arg, traj_path_arg)
-
-    @pytest.fixture()
-    def imd_u(self, topol_path_arg, tmp_path):
-        tmp_u = mda.Universe(topol_path_arg, "imd://localhost:8888")
-        with mda.Writer(
-            f"{tmp_path.as_posix()}/imd_test_traj.trr", tmp_u.atoms.n_atoms
-        ) as w:
-            for ts in tmp_u.trajectory:
-                w.write(tmp_u.atoms)
-        imd_u = mda.Universe(
-            topol_path_arg, f"{tmp_path.as_posix()}/imd_test_traj.trr"
+def load_true_universe(topol_path, traj_path):
+    if topol_path.endswith(".data"):
+        return mda.Universe(
+            topol_path,
+            traj_path,
+            atom_style="id type x y z",
+            convert_units=False,
         )
-        yield imd_u
+    return mda.Universe(topol_path, traj_path)
 
-    def test_compare_imd_to_true_traj(self, true_u, imd_u, first_frame_arg):
 
-        for i in range(first_frame_arg, len(true_u.trajectory)):
+def load_imd_universe(topol_path, tmp_path):
+    # Pass atom_style (ignored if not using LAMMPS topol)
+    tmp_u = mda.Universe(
+        topol_path,
+        "imd://localhost:8888",
+        atom_style="id type x y z",
+    )
+    tmp_traj_file = f"{tmp_path}/imd_test_traj.trr"
+    with mda.Writer(tmp_traj_file, tmp_u.atoms.n_atoms) as w:
+        for ts in tmp_u.trajectory:
+            w.write(tmp_u.atoms)
+    time.sleep(10)  # Give MPI ranks a chance to release FD
+    return mda.Universe(topol_path, tmp_traj_file, atom_style="id type x y z")
+
+
+def test_compare_imd_to_true_traj_vel(imd_u, true_u_vel, first_frame):
+    for i in range(first_frame, len(true_u_vel.trajectory)):
+        # Manually convert unit
+        assert_allclose_with_logging(
+            true_u_vel.trajectory[i].positions * 20.45482706,
+            imd_u.trajectory[i - first_frame].velocities,
+            atol=1e-03,
+        )
+
+
+def test_compare_imd_to_true_traj_forces(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,
+        )
+
+
+def test_compare_imd_to_true_traj(imd_u, true_u, first_frame, vel, force, dt):
+    for i in range(first_frame, len(true_u.trajectory)):
+        assert_allclose(
+            true_u.trajectory[i].time,
+            imd_u.trajectory[i - first_frame].time,
+            atol=1e-03,
+        )
+        if dt:
             assert_allclose(
-                true_u.trajectory[i].time,
-                imd_u.trajectory[i - first_frame_arg].time,
+                true_u.trajectory[i].dt,
+                imd_u.trajectory[i - first_frame].dt,
                 atol=1e-03,
             )
-            assert_allclose(
-                true_u.trajectory[i].data["step"],
-                imd_u.trajectory[i - first_frame_arg].data["step"],
+        assert_allclose(
+            true_u.trajectory[i].data["step"],
+            imd_u.trajectory[i - first_frame].data["step"],
+        )
+        assert_allclose_with_logging(
+            true_u.trajectory[i].dimensions,
+            imd_u.trajectory[i - first_frame].dimensions,
+            atol=1e-03,
+        )
+        assert_allclose_with_logging(
+            true_u.trajectory[i].positions,
+            imd_u.trajectory[i - first_frame].positions,
+            atol=1e-03,
+        )
+        if vel:
+            assert_allclose_with_logging(
+                true_u.trajectory[i].velocities,
+                imd_u.trajectory[i - first_frame].velocities,
+                atol=1e-03,
             )
-            if true_u.trajectory[i].dimensions is not None:
-                assert_allclose_with_logging(
-                    true_u.trajectory[i].dimensions,
-                    imd_u.trajectory[i - first_frame_arg].dimensions,
-                    atol=1e-03,
-                )
-            if true_u.trajectory[i].has_positions:
-                assert_allclose_with_logging(
-                    true_u.trajectory[i].positions,
-                    imd_u.trajectory[i - first_frame_arg].positions,
-                    atol=1e-03,
-                )
-            if true_u.trajectory[i].has_velocities:
-                assert_allclose_with_logging(
-                    true_u.trajectory[i].velocities,
-                    imd_u.trajectory[i - first_frame_arg].velocities,
-                    atol=1e-03,
-                )
-            if true_u.trajectory[i].has_forces:
-                assert_allclose_with_logging(
-                    true_u.trajectory[i].forces,
-                    imd_u.trajectory[i - first_frame_arg].forces,
-                    atol=1e-03,
-                )
+        if force:
+            assert_allclose_with_logging(
+                true_u.trajectory[i].forces,
+                imd_u.trajectory[i - first_frame].forces,
+                atol=1e-03,
+            )
+
+
+def main():
+    parser = argparse.ArgumentParser(description="IMDv3 Integration Test Tool")
+    parser.add_argument(
+        "--topol_path", required=True, help="Path to topology file"
+    )
+    parser.add_argument(
+        "--traj_path", required=True, help="Path to trajectory file"
+    )
+    parser.add_argument(
+        "--vel_path",
+        required=False,
+        help="Path to velocities trajectory file (NAMD only)",
+    )
+    parser.add_argument(
+        "--force_path",
+        required=False,
+        help="Path to forces trajectory file (NAMD only)",
+    )
+    parser.add_argument(
+        "--first_frame",
+        type=int,
+        required=True,
+        help="First frame to compare (0 for GROMACS and NAMD, 1 for LAMMPS)",
+    )
+    parser.add_argument(
+        "--tmp_path", default=".", help="Temporary directory for IMD traj"
+    )
+
+    args = parser.parse_args()
+
+    print(
+        "Writing IMD trajectory to temporary directory...\n===================="
+    )
+    imd_u = load_imd_universe(args.topol_path, args.tmp_path)
+
+    print("Loading source of truth trajectory...\n====================")
+    true_u = load_true_universe(args.topol_path, args.traj_path)
+
+    try:
+        print("Comparing trajectories...\n====================")
+        vel_in_trr = args.vel_path is None
+        force_in_trr = args.force_path is None
+        dt_in_trr = not args.topol_path.endswith(".data")
+
+        test_compare_imd_to_true_traj(
+            imd_u,
+            true_u,
+            args.first_frame,
+            vel_in_trr,
+            force_in_trr,
+            dt_in_trr,
+        )
+
+        if args.vel_path is not None:
+            print(
+                "Loading source of truth velocity trajectory...\n===================="
+            )
+            true_vel = load_true_universe(args.topol_path, args.vel_path)
+            print("Comparing velocities...")
+            test_compare_imd_to_true_traj_vel(
+                imd_u, true_vel, args.first_frame
+            )
+
+        if args.force_path is not None:
+            print(
+                "Loading source of truth force trajectory...\n===================="
+            )
+            true_force = load_true_universe(args.topol_path, args.force_path)
+            print("Comparing forces...")
+            test_compare_imd_to_true_traj_forces(
+                imd_u, true_force, args.first_frame
+            )
+
+        print("All tests passed!")
+
+    except AssertionError as e:
+        logger.error("Comparison failed!")
+        print(f"Test failed: {e}")
+        raise e
+
+
+if __name__ == "__main__":
+    main()

{imdclient-0.1.3.dist-info → imdclient-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: imdclient
-Version: 0.1.3
+Version: 0.1.4
 Summary: Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
 Author-email: Lawson <ljwoods2@asu.edu>
 Maintainer-email: Lawson <ljwoods2@asu.edu>

imdclient-0.1.4.dist-info/RECORD

@@ -0,0 +1,57 @@
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+imdclient/utils.py,sha256=VWxk4vQ6hzxoYRu-8Ge8fJG-EitJwgJR93wOWCvzY-0,3308
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+imdclient-0.1.4.dist-info/AUTHORS.md,sha256=R4JTI7mrgL1WYgfyuAv4quw0e0oLQGVjWcMQa-UXJlE,652
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+imdclient-0.1.4.dist-info/RECORD,,

imdclient-0.1.3.dist-info/RECORD

@@ -1,42 +0,0 @@
-imdclient/IMD.py,sha256=-ySUiRBumVEKyZU3UXXNywajtVnERQhtP4ama3guCR4,3767
-imdclient/IMDClient.py,sha256=6p8nLe70d-eUdsJ6QNcpc8V1Mp-ozD7mhB35_p6Owuc,33330
-imdclient/IMDProtocol.py,sha256=jm7ehwfDCcs-zWHjZ2V2KpAWdGhD4JSy7RVtCSF0818,4045
-imdclient/__init__.py,sha256=Pa5h6Fjyvyxf3ECzO43pcmLm3Vk-vOuEb5Gi6TDWhds,339
-imdclient/backends.py,sha256=QmHjwYbmvFVHz-uFgpSOA0UmZTZqiMGqWMO7B8wr1zs,10368
-imdclient/results.py,sha256=2MyjFdQMW7BfiHhG5X6wQwMVrF_0mKYFnv907lgLMas,9920
-imdclient/streamanalysis.py,sha256=Qq0h_WPO-wb0_lP8jTRHe0HX7UDZNgJFA6C4PZdUmK8,38385
-imdclient/streambase.py,sha256=rwhdyC2V3_9pSz_6rNwjSc4MNToI9S318OH7AH0arHA,6176
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