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CENSO 2.1 #60

Merged
merged 79 commits into from
Oct 21, 2024
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decddf5
prepare reload capability
lmseidler Sep 26, 2024
ba5119d
reload capability
lmseidler Sep 26, 2024
8041d73
tm proc basic setup
lmseidler Sep 27, 2024
f70dc55
tm proc basic setup
lmseidler Sep 27, 2024
20f4b66
tm prep almost done
lmseidler Sep 27, 2024
860a4d8
sm/prog compatibility check
lmseidler Sep 30, 2024
a76fa13
settings case insensitive
lmseidler Sep 30, 2024
c3d9605
tm solvation cosmo + dcosmors done, cosmors basics
lmseidler Sep 30, 2024
129450a
optimization additional sort
lmseidler Sep 30, 2024
4ecf9e0
cosmors gsolv calculation basics
lmseidler Oct 1, 2024
1fca7b4
tm gsolv sp calls
lmseidler Oct 1, 2024
e15de65
change on how to copy mo
lmseidler Oct 2, 2024
36c7292
turbomole single-point
lmseidler Oct 2, 2024
b6bb360
cosmors done
lmseidler Oct 2, 2024
5f01e6b
tm xtb_opt done
lmseidler Oct 2, 2024
e8684dc
tm nmr done
lmseidler Oct 4, 2024
30c9b57
property calculations boilerplate class
lmseidler Oct 4, 2024
6e31195
cosmors gsolv calculation done
lmseidler Oct 4, 2024
94d7958
property boilerplate
lmseidler Oct 4, 2024
0e18c0a
hopefully removed all faulty format strings
lmseidler Oct 4, 2024
039e439
fixed missing tm import
lmseidler Oct 4, 2024
1ef704a
next try
lmseidler Oct 4, 2024
18b2014
next try 2
lmseidler Oct 4, 2024
a997032
fixed cml parser
lmseidler Oct 4, 2024
ec6d959
parallel call fix
lmseidler Oct 4, 2024
5d0fe6d
loglevel setting cml
lmseidler Oct 4, 2024
6577552
proper environment variable setting (no strings allowed)
lmseidler Oct 4, 2024
17f39c6
fixed missing cefine call
lmseidler Oct 4, 2024
19ea0a2
fixed outdated code?
lmseidler Oct 4, 2024
e3770bf
fixed usage of 'solvent'
lmseidler Oct 4, 2024
b1143f0
fixed solvation in tm prep
lmseidler Oct 4, 2024
707fe2a
tm cefine prep change
lmseidler Oct 7, 2024
bd8e52c
formatting
lmseidler Oct 7, 2024
1db9095
formatting again
lmseidler Oct 7, 2024
29080ee
log level adjustable via cml
lmseidler Oct 9, 2024
afbc53c
cefine fix?
lmseidler Oct 9, 2024
b96a4f5
added basis lookup for turbomole
lmseidler Oct 9, 2024
662f78e
tm encoding
lmseidler Oct 10, 2024
b0c9d05
cefine proper error handling
lmseidler Oct 10, 2024
62f06f9
subprocess error reraise + removed tm file encoding
lmseidler Oct 10, 2024
e61d011
coord file generation order fix
lmseidler Oct 10, 2024
ef4c647
turbomole gcp + d4 bug avoided
lmseidler Oct 10, 2024
2816763
turbomole gcp + d4 bug avoided for real now
lmseidler Oct 10, 2024
68b544e
r2scan-3c turbomole grid fix
lmseidler Oct 10, 2024
b0cb84f
tm solv prep missing newlines fix
lmseidler Oct 10, 2024
e9e87fc
tm copy mo moved before prep
lmseidler Oct 11, 2024
354fa9a
tm xtbopt fixed
lmseidler Oct 11, 2024
364567d
new handling for solvent and dfa availability check
lmseidler Oct 11, 2024
b7fc608
small fix 1
lmseidler Oct 11, 2024
78da17c
small fix 2
lmseidler Oct 11, 2024
e32b0b0
small fix 3
lmseidler Oct 11, 2024
61bf0ff
small fix 4
lmseidler Oct 11, 2024
222cb44
small fix 5
lmseidler Oct 11, 2024
59670ae
small fix 6
lmseidler Oct 11, 2024
44e8a27
small fix 7
lmseidler Oct 11, 2024
452364d
'legacy' load balancing for using tm
lmseidler Oct 14, 2024
ca1c03f
part json dump contains part name
lmseidler Oct 14, 2024
ceb7877
read_output reads new jsons correctly
lmseidler Oct 14, 2024
2fcc48a
read_output error fixed
lmseidler Oct 14, 2024
ee03bd8
small fix
lmseidler Oct 14, 2024
80001a3
small fix 2
lmseidler Oct 14, 2024
5388b97
improved _set_energy for property_calculator
lmseidler Oct 14, 2024
a411b4e
tm nmr prep fix
lmseidler Oct 14, 2024
7db1faf
tm nmr nucsel fix
lmseidler Oct 16, 2024
f30f58f
tm gcp+d4 bug switching disp/gcp off decision
lmseidler Oct 16, 2024
f9150db
typo fix
lmseidler Oct 16, 2024
e992f78
nmr grid settings fix
lmseidler Oct 16, 2024
65069b3
cosmors redone
lmseidler Oct 17, 2024
6337279
copy_mo/prep order never violated (hopefully)
lmseidler Oct 17, 2024
d4515ae
write_results for screening fixed when using gsolv
lmseidler Oct 17, 2024
9c3fe87
screening fixes
lmseidler Oct 17, 2024
92c7cff
better check for explicit gsolv inclusion
lmseidler Oct 17, 2024
b91f3e4
screening refienement writeresults final fix
lmseidler Oct 17, 2024
cdb4b96
small fix
lmseidler Oct 17, 2024
914874b
fixed dummy functionality + not available for tm
lmseidler Oct 17, 2024
5f25834
tm nmr fconly
lmseidler Oct 18, 2024
a7cdd59
finalized basic tm implementation
lmseidler Oct 21, 2024
47b3705
small fix
lmseidler Oct 21, 2024
a9feee8
Merge branch 'main' into dev
lmseidler Oct 21, 2024
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read_output error fixed
lmseidler committed Oct 14, 2024
commit 2fcc48abb8b8981db551c3307976d1ba2d2a1441
11 changes: 6 additions & 5 deletions src/censo/ensembledata.py
Original file line number Diff line number Diff line change
@@ -86,16 +86,17 @@ def read_output(self, outpath: str) -> None:
data = json.load(file)

# Check if all conformers from the current ensemble are also found in the output data
for item in data.items():
for partname, results in data.values():
# First level of json output is the part name (loop iterates through all parts in the json file)
if not all(conf.name in item for conf in self.conformers):
# .values() are the results of each part
if not all(conf.name in results for conf in self.conformers):
raise RuntimeError(
"Not all conformers from the current ensemble are found in the output data."
)

# Update results dict for the conformers
for conf in self.conformers:
conf.results.update(data[conf.name])
# Update results dict for the conformers
for conf in self.conformers:
conf.results[partname].update(results[conf.name])

def read_input(
self,