In [1]: import os
In [2]: import pandas as pd
In [3]: from nanoCAT.recipes import run_fast_sigma
In [4]: smiles_list = ["CO[H]", "CCO[H]", "CCCO[H]"]
In [5]: solvent_dict = {"octadecene": "./1-Octadecene.coskf", "dioctylether": "./Di-n-octyl_ether.coskf"}
In [6]: output_dir: str = "."
In [7]: ams_dir: str = "C:\SCMTMP"
In [8]: run_fast_sigma(smiles_list, solvent_dict, output_dir=output_dir, ams_dir=ams_dir)
However the associated plamsjobs systematically fail and I only get NaN in the pandas dataframe.
Here is the plamsjob.err :
ERROR: COSMO input file does not existC:\SCMTMP\fc8842c641d9150647f928e6c294ce26dd51ecae5ba30b114a78ddedcd398815.compkf
ERROR DETECTED
and the plamsjob.in :
RSParameters
HB_HNOF
HB_TEMP
FAST
COMBI2005
Eta -9.65
Lambda 0.13
aeff 6.94
aprime 1510.0
chb 8850.0
chortf 0.816
fcorr 2.802
omega -0.212
rav 0.4
sigmahbond 0.00854
end
Dispersion
Br -0.055
C -0.0356
Cl -0.0485
F -0.026
H -0.034
I -0.062
N -0.0224
O -0.0333
P -0.045
S -0.052
Si -0.04
end
Technical
bpconv 1e-6
bpmaxiter 40
ehdeltaT 1.0
maxiter 10000
rsconv 1e-7
solconv 1e-5
solmaxiter 40
solxilarge 0.99
end
compound C:/AMS2023.104//atomicdata/ADFCRS/1-Octanol.coskf
density 0.824
flashpoint 354.0
frac1 0.725
meltingpoint 257.0
pvap 1.01325
tvap 468.0
end
compound C:/AMS2023.104//atomicdata/ADFCRS/Water.coskf
density 0.997
frac1 0.275
frac2 1.0
hfusion 1.436
meltingpoint 273.15
pvap 1.01325
tvap 373.15
end
compound "C:\SCMTMP\fc8842c641d9150647f928e6c294ce26dd51ecae5ba30b114a78ddedcd398815.compkf"
compkffile
end
compound "C:\SCMTMP\ab1de819ede91df490e6441934decfa9041b49f91d6bbadbba4df634ccff57fa.compkf"
compkffile
end
compound "C:\SCMTMP\462b618a7419d00dd59fb15aed29e14bafd4a7d7d862f15758cac9c392890247.compkf"
compkffile
end
property logp
volumequotient 6.766
end
I'm trying to run the fast_sigma recipe according to the small example provided in the documentation: https://cat.readthedocs.io/en/latest/12_11_recipes.html
In [1]: import os In [2]: import pandas as pd In [3]: from nanoCAT.recipes import run_fast_sigma In [4]: smiles_list = ["CO[H]", "CCO[H]", "CCCO[H]"] In [5]: solvent_dict = {"octadecene": "./1-Octadecene.coskf", "dioctylether": "./Di-n-octyl_ether.coskf"} In [6]: output_dir: str = "." In [7]: ams_dir: str = "C:\SCMTMP" In [8]: run_fast_sigma(smiles_list, solvent_dict, output_dir=output_dir, ams_dir=ams_dir)
However the associated plamsjobs systematically fail and I only get NaN in the pandas dataframe.
Here is the plamsjob.err :
and the plamsjob.in :