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Added an example run_REXEE_log.txt and a unit test for get_swaps
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wehs7661 committed Apr 8, 2024
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6 changes: 3 additions & 3 deletions ensemble_md/analysis/analyze_traj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def stitch_time_series(files, rep_trajs, shifts=None, dhdl=True, col_idx=-1, sav
traj = list(np.array(traj) + shifts[shift_idx])
else:
traj = np.loadtxt(files_sorted[i][j], comments=['#', '@'])[:, col_idx]

if j != n_iter - 1:
traj = traj[:-1]

Expand Down Expand Up @@ -180,7 +180,7 @@ def stitch_time_series_for_sim(files, shifts, dhdl=True, col_idx=-1, save=True):
traj = traj[:-1] # remove the last frame, which is the same as the first of the next time series.

trajs[i].extend(traj)

# All segments for the same replica should have the same shift
trajs[i] = list(np.array(trajs[i]) + shifts[i])

Expand Down Expand Up @@ -835,7 +835,7 @@ def plot_g_vecs(g_vecs, refs=None, refs_err=None, plot_rmse=True):

def get_swaps(REXEE_log='run_REXEE_log.txt'):
"""
For each replica, identifies the states where exchanges were proposed and accepted.
For each replica, identifies the states involved in proposed and accepted exchanges.
(Todo: We should be able to only use :code:`rep_trajs.npy` and :code:`state_trajs.npy`
instead of parsing the REXEE log file to reach the same goal.)
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363 changes: 363 additions & 0 deletions ensemble_md/tests/data/run_REXEE_log.txt
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@@ -0,0 +1,363 @@
Current time: 19/06/2023 04:08:37
Command line: /jet/home/wehs7661/.local/python3.9/bin/run_EEXE

Important parameters of EXEE
============================
Python version: 3.9.12 (main, Feb 28 2023, 14:59:18)
[GCC 10.2.0]
GROMACS executable: /jet/home/wehs7661/pkgs/gromacs/2022.5/bin/gmx
GROMACS version: 2022.5-dev-20230428-fdf57150ad
ensemble_md version: 0.6.0+40.gba0d9e6.dirty
Simulation inputs: anthracene.gro, anthracene.top, expanded.mdp
Verbose log file: True
Proposal scheme: exhaustive
Acceptance scheme for swapping simulations: metropolis
Whether to perform weight combination: False
Histogram cutoff: -1
Number of replicas: 4
Number of iterations: 12500
Number of attempted swaps in one exchange interval: N^3
Length of each replica: 4.0 ps
Frequency for checkpointing: 100 iterations
Total number of states: 8
Additional grompp arguments: None
Additional runtime arguments: {'-nt': '16', '-ntmpi': '1'}
Alchemical ranges of each replica in EEXE:
- Replica 0: States [0, 1, 2, 3, 4]
- Replica 1: States [1, 2, 3, 4, 5]
- Replica 2: States [2, 3, 4, 5, 6]
- Replica 3: States [3, 4, 5, 6, 7]

Iteration 0: 0.0 - 4.0 ps
===========================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 1, (coul, vdw) = (0.18,)
Simulation 1: Global state 2, (coul, vdw) = (0.42,)
Simulation 2: Global state 3, (coul, vdw) = (0.57,)
Simulation 3: Global state 4, (coul, vdw) = (0.68,)

Parsing sim_0/iteration_0/md.log ...
Parsing sim_1/iteration_0/md.log ...
Parsing sim_2/iteration_0/md.log ...
Parsing sim_3/iteration_0/md.log ...

Swappable pairs: [(0, 1), (1, 2), (2, 3)]

Proposed swap: (2, 3)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 1.91 kT, U^j_m - U^j_n = 6.93 kT, Total dU: 8.84 kT
g^i_n - g^i_m = 0.43 kT, g^j_m - g^j_n = -0.43 kT, Total dg: 0.00 kT
Acceptance rate: 0.000 / Random number drawn: 0.212
Swap rejected!
Current list of configurations: [0, 1, 2, 3]

Remaining swappable pairs: [(0, 1)]

Proposed swap: (0, 1)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 5.12 kT, U^j_m - U^j_n = 1.53 kT, Total dU: 6.65 kT
g^i_n - g^i_m = 4.94 kT, g^j_m - g^j_n = -4.94 kT, Total dg: 0.00 kT
Acceptance rate: 0.001 / Random number drawn: 0.958
Swap rejected!
Current list of configurations: [0, 1, 2, 3]

The finally adopted swap pattern: [0, 1, 2, 3]
The list of configurations sampled in each replica in the next iteration: [0, 1, 2, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 1: 4.0 - 8.0 ps
===========================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 1, (coul, vdw) = (0.18,)
Simulation 1: Global state 1, (coul, vdw) = (0.18,)
Simulation 2: Global state 3, (coul, vdw) = (0.57,)
Simulation 3: Global state 6, (coul, vdw) = (0.86,)

Parsing sim_0/iteration_1/md.log ...
Parsing sim_1/iteration_1/md.log ...
Parsing sim_2/iteration_1/md.log ...
Parsing sim_3/iteration_1/md.log ...

Swappable pairs: [(0, 1), (2, 3)]

Proposed swap: (0, 1)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 0.00 kT, U^j_m - U^j_n = 0.00 kT, Total dU: 0.00 kT
g^i_n - g^i_m = 0.00 kT, g^j_m - g^j_n = 0.00 kT, Total dg: 0.00 kT
Acceptance rate: 1.000 / Random number drawn: 0.047
Swap accepted!
Current list of configurations: [1, 0, 2, 3]

Remaining swappable pairs: [(2, 3)]

Proposed swap: (2, 3)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 8.64 kT, U^j_m - U^j_n = 41.64 kT, Total dU: 50.28 kT
g^i_n - g^i_m = -5.23 kT, g^j_m - g^j_n = 5.23 kT, Total dg: 0.00 kT
Acceptance rate: 0.000 / Random number drawn: 0.347
Swap rejected!
Current list of configurations: [1, 0, 2, 3]

The finally adopted swap pattern: [1, 0, 2, 3]
The list of configurations sampled in each replica in the next iteration: [1, 0, 2, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 2: 8.0 - 12.0 ps
============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 1, (coul, vdw) = (0.18,)
Simulation 1: Global state 5, (coul, vdw) = (0.76,)
Simulation 2: Global state 4, (coul, vdw) = (0.68,)
Simulation 3: Global state 7, (coul, vdw) = (1.0,)

Parsing sim_0/iteration_2/md.log ...
Parsing sim_1/iteration_2/md.log ...
Parsing sim_2/iteration_2/md.log ...
Parsing sim_3/iteration_2/md.log ...

n_ex is set back to 1 since there is only 1 swappable pair.
Swappable pairs: [(1, 2)]

Proposed swap: (1, 2)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 9.19 kT, U^j_m - U^j_n = -2.31 kT, Total dU: 6.88 kT
g^i_n - g^i_m = 1.45 kT, g^j_m - g^j_n = -1.45 kT, Total dg: 0.00 kT
Acceptance rate: 0.001 / Random number drawn: 0.303
Swap rejected!
Current list of configurations: [1, 0, 2, 3]

The finally adopted swap pattern: [0, 1, 2, 3]
The list of configurations sampled in each replica in the next iteration: [1, 0, 2, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 3: 12.0 - 16.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 0, (coul, vdw) = (0.0,)
Simulation 1: Global state 5, (coul, vdw) = (0.76,)
Simulation 2: Global state 6, (coul, vdw) = (0.86,)
Simulation 3: Global state 7, (coul, vdw) = (1.0,)

Parsing sim_0/iteration_3/md.log ...
Parsing sim_1/iteration_3/md.log ...
Parsing sim_2/iteration_3/md.log ...
Parsing sim_3/iteration_3/md.log ...

Swappable pairs: []

The finally adopted swap pattern: [0, 1, 2, 3]
The list of configurations sampled in each replica in the next iteration: [1, 0, 2, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 4: 16.0 - 20.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 1, (coul, vdw) = (0.18,)
Simulation 1: Global state 1, (coul, vdw) = (0.18,)
Simulation 2: Global state 3, (coul, vdw) = (0.57,)
Simulation 3: Global state 6, (coul, vdw) = (0.86,)

Parsing sim_0/iteration_4/md.log ...
Parsing sim_1/iteration_4/md.log ...
Parsing sim_2/iteration_4/md.log ...
Parsing sim_3/iteration_4/md.log ...

Swappable pairs: [(0, 1), (2, 3)]

Proposed swap: (0, 1)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 0.00 kT, U^j_m - U^j_n = 0.00 kT, Total dU: 0.00 kT
g^i_n - g^i_m = 0.00 kT, g^j_m - g^j_n = 0.00 kT, Total dg: 0.00 kT
Acceptance rate: 1.000 / Random number drawn: 0.601
Swap accepted!
Current list of configurations: [0, 1, 2, 3]

Remaining swappable pairs: [(2, 3)]

Proposed swap: (2, 3)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 7.79 kT, U^j_m - U^j_n = 52.74 kT, Total dU: 60.53 kT
g^i_n - g^i_m = -5.23 kT, g^j_m - g^j_n = 5.23 kT, Total dg: 0.00 kT
Acceptance rate: 0.000 / Random number drawn: 0.530
Swap rejected!
Current list of configurations: [0, 1, 2, 3]

The finally adopted swap pattern: [1, 0, 2, 3]
The list of configurations sampled in each replica in the next iteration: [0, 1, 2, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 5: 20.0 - 24.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 2, (coul, vdw) = (0.42,)
Simulation 1: Global state 4, (coul, vdw) = (0.68,)
Simulation 2: Global state 2, (coul, vdw) = (0.42,)
Simulation 3: Global state 6, (coul, vdw) = (0.86,)

Parsing sim_0/iteration_5/md.log ...
Parsing sim_1/iteration_5/md.log ...
Parsing sim_2/iteration_5/md.log ...
Parsing sim_3/iteration_5/md.log ...

Swappable pairs: [(0, 1), (0, 2), (1, 2)]

Proposed swap: (0, 2)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 0.00 kT, U^j_m - U^j_n = 0.00 kT, Total dU: 0.00 kT
g^i_n - g^i_m = 0.00 kT, g^j_m - g^j_n = 0.00 kT, Total dg: 0.00 kT
Acceptance rate: 1.000 / Random number drawn: 0.883
Swap accepted!
Current list of configurations: [2, 1, 0, 3]

Remaining swappable pairs: []

The finally adopted swap pattern: [2, 1, 0, 3]
The list of configurations sampled in each replica in the next iteration: [2, 1, 0, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 6: 24.0 - 28.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 0, (coul, vdw) = (0.0,)
Simulation 1: Global state 4, (coul, vdw) = (0.68,)
Simulation 2: Global state 2, (coul, vdw) = (0.42,)
Simulation 3: Global state 7, (coul, vdw) = (1.0,)

Parsing sim_0/iteration_6/md.log ...
Parsing sim_1/iteration_6/md.log ...
Parsing sim_2/iteration_6/md.log ...
Parsing sim_3/iteration_6/md.log ...

n_ex is set back to 1 since there is only 1 swappable pair.
Swappable pairs: [(1, 2)]

Proposed swap: (1, 2)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 11.12 kT, U^j_m - U^j_n = 6.74 kT, Total dU: 17.86 kT
g^i_n - g^i_m = -2.63 kT, g^j_m - g^j_n = 2.63 kT, Total dg: 0.00 kT
Acceptance rate: 0.000 / Random number drawn: 0.041
Swap rejected!
Current list of configurations: [2, 1, 0, 3]

The finally adopted swap pattern: [0, 1, 2, 3]
The list of configurations sampled in each replica in the next iteration: [2, 1, 0, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 7: 28.0 - 32.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 0, (coul, vdw) = (0.0,)
Simulation 1: Global state 1, (coul, vdw) = (0.18,)
Simulation 2: Global state 4, (coul, vdw) = (0.68,)
Simulation 3: Global state 6, (coul, vdw) = (0.86,)

Parsing sim_0/iteration_7/md.log ...
Parsing sim_1/iteration_7/md.log ...
Parsing sim_2/iteration_7/md.log ...
Parsing sim_3/iteration_7/md.log ...

n_ex is set back to 1 since there is only 1 swappable pair.
Swappable pairs: [(2, 3)]

Proposed swap: (2, 3)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 0.02 kT, U^j_m - U^j_n = 17.39 kT, Total dU: 17.41 kT
g^i_n - g^i_m = -5.66 kT, g^j_m - g^j_n = 5.66 kT, Total dg: 0.00 kT
Acceptance rate: 0.000 / Random number drawn: 0.494
Swap rejected!
Current list of configurations: [2, 1, 0, 3]

The finally adopted swap pattern: [0, 1, 2, 3]
The list of configurations sampled in each replica in the next iteration: [2, 1, 0, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 8: 32.0 - 36.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

Below are the final states being visited:
Simulation 0: Global state 1, (coul, vdw) = (0.18,)
Simulation 1: Global state 2, (coul, vdw) = (0.42,)
Simulation 2: Global state 2, (coul, vdw) = (0.42,)
Simulation 3: Global state 7, (coul, vdw) = (1.0,)

Parsing sim_0/iteration_8/md.log ...
Parsing sim_1/iteration_8/md.log ...
Parsing sim_2/iteration_8/md.log ...
Parsing sim_3/iteration_8/md.log ...

Swappable pairs: [(0, 1), (1, 2)]

Proposed swap: (1, 2)
Proposing a move from (x^i_m, x^j_n) to (x^i_n, x^j_m) ...
U^i_n - U^i_m = 0.00 kT, U^j_m - U^j_n = 0.00 kT, Total dU: 0.00 kT
g^i_n - g^i_m = 0.00 kT, g^j_m - g^j_n = 0.00 kT, Total dg: 0.00 kT
Acceptance rate: 1.000 / Random number drawn: 0.254
Swap accepted!
Current list of configurations: [2, 0, 1, 3]

Remaining swappable pairs: []

The finally adopted swap pattern: [0, 2, 1, 3]
The list of configurations sampled in each replica in the next iteration: [2, 0, 1, 3]

Note: No histogram correction will be performed.
Note: No weight combination will be performed.

Iteration 9: 36.0 - 40.0 ps
=============================
Generating a TPR file on rank 0 ...
Running an EXE simulation on rank 0 ...

----- Saving .npy files to checkpoint the simulation ---

Summary of the simulation ensemble
==================================
Simulation status:
- Rep 0: The weights were fixed throughout the simulation.
- Rep 1: The weights were fixed throughout the simulation.
- Rep 2: The weights were fixed throughout the simulation.
- Rep 3: The weights were fixed throughout the simulation.

Time elapsed: xx hour(s) xx minute(s) xx second(s)
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