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jaclark5 committed Sep 19, 2024
1 parent f6ad696 commit 752cd64
Showing 1 changed file with 21 additions and 11 deletions.
32 changes: 21 additions & 11 deletions src/alchemlyb/parsing/lammps.py
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
LAMMPS, `fix adapt/fep <https://docs.lammps.org/fix_adapt_fep.html>`_ changes :math:`\lambda` and
`compute fep <https://docs.lammps.org/compute_fep.html>`_ changes :math:`\lambda'`.
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

Expand Down Expand Up @@ -59,7 +59,8 @@ def beta_from_units(T, units):
ValueError
If unit string is not recognized.
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""
if units == "real": # E in kcal/mol, T in K
beta = 1 / (R_kJmol * kJ2kcal * T)
Expand Down Expand Up @@ -105,7 +106,8 @@ def energy_from_units(units):
ValueError
If unit string is not recognized.
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""
if units == "real": # E in kcal/mol, Vol in Å^3, pressure in atm
beta = constants.atm * constants.angstrom**3 / 1e+3 * kJ2kcal * constants.N_A
Expand Down Expand Up @@ -153,7 +155,8 @@ def _tuple_from_filename(filename, separator="_", indices=[2, 3], prec=4):
tuple[float]
Tuple of lambda values
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

name_array = ".".join(os.path.split(filename)[-1].split(".")[:-1]).split(separator)
Expand Down Expand Up @@ -199,7 +202,8 @@ def _lambda_from_filename(filename, separator="_", index=-1, prec=4):
float
Lambda prime value
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""
name_array = ".".join(os.path.split(filename)[-1].split(".")[:-1]).split(separator)
try:
Expand Down Expand Up @@ -233,7 +237,8 @@ def _get_bar_lambdas(fep_files, indices=[2, 3], prec=4, force=False):
lambda_pairs : list
List of tuples containing two floats, lambda and lambda'.
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

lambda_pairs = [
Expand Down Expand Up @@ -387,7 +392,8 @@ def extract_u_nk_from_u_n(
- temperature in K
- energy unit in kT
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""
# Collect Files
files = glob.glob(fep_files)
Expand Down Expand Up @@ -572,7 +578,8 @@ def extract_u_nk(
- temperature in K
- energy unit in kT
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

# Collect Files
Expand Down Expand Up @@ -832,7 +839,8 @@ def extract_dHdl_from_u_n(
- temperature in K or dimensionless
- energy unit in kT
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

# Collect Files
Expand Down Expand Up @@ -941,7 +949,8 @@ def extract_dHdl(
- temperature in K or dimensionless
- energy unit in kT
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

# Collect Files
Expand Down Expand Up @@ -1124,7 +1133,8 @@ def extract_H(
- temperature in K or dimensionless
- energy unit in kT
.. versionadded:: 2.4.0
.. versionadded:: 2.4.1
"""

# Collect Files
Expand Down

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