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Add pV and U to reduced potential when they are given #62

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merged 11 commits into from
Nov 26, 2018
Merged

Add pV and U to reduced potential when they are given #62

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dcad2b8
Add pV and U to reduced potential when they are given
harlor Oct 21, 2018
037bee4
Update TestStatisticalInefficiency after u_nk parser update
harlor Oct 21, 2018
65159f7
If Potential energy is given add it to reduced potential
harlor Nov 4, 2018
27cb260
Add tests for the calculation of the reduced potential
harlor Nov 16, 2018
0af3093
Use assert_almost_equal instead of assert
harlor Nov 16, 2018
837c266
Merge branch 'master' into reduced_potential_pr
harlor Nov 17, 2018
fe014b3
Use decimal precision 6 for float comparison in tests
harlor Nov 17, 2018
886b0ef
Use reasonable decimal precision for float comparison in tests
harlor Nov 17, 2018
f8ad375
Compare with ordered datasets
harlor Nov 17, 2018
74333c5
Remove unnecessary type conversion to float
harlor Nov 19, 2018
bfbe0b0
Merge branch 'master' into reduced_potential_pr
dotsdl Nov 23, 2018
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31 changes: 21 additions & 10 deletions src/alchemlyb/parsing/gmx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,9 @@ def extract_u_nk(xvg, T):

"""

col_match = r"\xD\f{}H \xl\f{}"
h_col_match = r"\xD\f{}H \xl\f{}"
pv_col_match = 'pV'
u_col_match = 'Total Energy'
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Checking the files you provided @harlor (https://userpage.fu-berlin.de/dominikwille/nvt300K.tgz), I see "Potential Energy (kJ/mol)" in the ti_0.xvg file. Should we also try and match that?

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@harlor harlor Nov 1, 2018 •
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@mrshirts explained that in #59 (comment). So I think we need the total energy.

I uploaded a dataset with total energy here: http://dominikwille.userpage.fu-berlin.de/nvt300K_u.tgz

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Okay, but I think depending on MDP options given to gromacs it's possible to have a dataset without "Total Energy" but with "Potential Energy". I was thinking that we could handle this in another PR with kwargs, but I don't believe this should be neglected.

Could you add a check for the existence of a "Potential Energy" column as you did for the "Total Energy" column, and if present, use this instead of the "Total Energy" column? That would satisfy me for the purposes of this PR

beta = 1/(k_b * T)

state, lambdas, statevec = _extract_state(xvg)
Expand All @@ -43,22 +45,31 @@ def extract_u_nk(xvg, T):
times = df[df.columns[0]]

# want to grab only dH columns
DHcols = [col for col in df.columns if (col_match in col)]
DHcols = [col for col in df.columns if (h_col_match in col)]
dH = df[DHcols]

# not entirely sure if we need to get potentials relative to
# the state actually sampled, but perhaps needed to stack
# samples from all states?
U = df[df.columns[1]]

# gromacs also gives us pV directly; need this for reduced potential
pV = df[df.columns[-1]]
pv_cols = [col for col in df.columns if (pv_col_match in col)]
pv = None
if pv_cols:
pv = df[pv_cols[0]]

# gromacs also gives us total energy U directly; need this for reduced potential
u_cols = [col for col in df.columns if (u_col_match in col)]
u = None
if u_cols:
u = df[u_cols[0]]

u_k = dict()
cols= list()
cols = list()
for col in dH:
u_col = eval(col.split('to')[1])
u_k[u_col] = beta * (dH[col].values + U.values + pV.values)
# calculate reduced potential u_k = dH + pV + U
u_k[u_col] = beta * dH[col].values
if pv_cols:
u_k[u_col] += beta * pv.values
if u_cols:
u_k[u_col] += beta * u.values
cols.append(u_col)

u_k = pd.DataFrame(u_k, columns=cols,
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2 changes: 1 addition & 1 deletion src/alchemlyb/tests/test_preprocessing.py
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Expand Up @@ -100,7 +100,7 @@ def slicer(self, *args, **kwargs):
(True, gmx_benzene_dHdl(), 2001), # 0.00: g = 1.0559445620585415
(True, gmx_benzene_u_nk(), 2001), # 'fep': g = 1.0560203916559594
(False, gmx_benzene_dHdl(), 3789),
(False, gmx_benzene_u_nk(), 3789),
(False, gmx_benzene_u_nk(), 3571),
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])
def test_conservative(self, data, size, conservative):
sliced = self.slicer(data, series=data.iloc[:, 0], conservative=conservative)
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