Comments (6)
commented on June 4, 2024
Here's the compressed version of the CB8.xyz input file that I used for the above run:
CB8.xyz.zip
If you're tempted to reproduce, please be aware that the run took 7.5 hrs with 12 threads on a 12-core mid2010 Mac Pro
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pprcht
commented on June 4, 2024
I don't think it is related to OMP stacksizes and -alpb. At this point where it crashes all calculations are done and only I/O is left. Have you checked the structures in crest_property.xyz? Maybe they broke and hence some reading/writing does not work
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commented on June 4, 2024
The example above is cucurbit[8]uril. There are only two structures in crest_property.xyz and they both seem to be intact - one is d8h symmetry, the other cs, at much higher energy, as expected. This same job (with -gbsa instead of -alpb) worked fine in 2.10.2.
In issue #15 you pointed out that the CREGEN data ends up in PROP/cregen.out.tmp. This certainly is the case for me with small guest molecules, but not with the larger CB8 host. Perhaps an array bound is being inadvertently violated during i/o now?
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pprcht
commented on June 4, 2024
As mentioned in the other issue I have updated the attached binary of the pre-release, but this problem/bug here still eludes me. However, the crest_property.xyz should be the final ensemble and all that is missing is sorting it, so maybe you could try to use crest coord --cregen crest_property.xyz. Although with only two structures the outcome of this is probably expectable...
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commented on June 4, 2024
Thanks for sharing the updated version but it still stops at the same place (this time with 3 structures). The final lines in the output file are:
---------------------------------------
Hessian calculations for all conformers
---------------------------------------
Performing calculations for 3 structures ...
1 2 3
done.
The separate cregen job on PROP/crest_property.xyz runs OK so this gives me the thermo data:
Command line input:
> crest CB8.xyz --cregen PROP/crest_property.xyz
--cregen : CREGEN standalone usage. Sorting file <PROP/crest_property.xyz>
=============================
# threads = 12
=============================
Using only the cregen sorting routine.
input file name : PROP/crest_property.xyz
output file name : PROP/crest_property.xyz.sorted
number of atoms : 144
number of points on xyz files : 3
RMSD threshold : 0.1250
Bconst threshold : 0.0100
population threshold : 0.0500
conformer energy window /kcal : 6.0000
# fragment in coord : 1
# bonds in reference structure : 168
number of reliable points : 3
reference state Etot : -286.136982583200
running RMSDs...
done.
number of doubles removed by rot/RMSD : 0
total number unique points considered further : 3
Erel/kcal Etot weight/tot conformer set degen origin
1 0.000 -286.13698 0.99352 0.99352 1 1
2 3.014 -286.13218 0.00617 0.00617 2 1
3 4.778 -286.12937 0.00031 0.00031 3 1
T /K : 298.15
E lowest : -286.13698
ensemble average energy (kcal) : 0.020
ensemble entropy (J/mol K, cal/mol K) : 0.336 0.080
ensemble free energy (kcal/mol) : -0.024
population of lowest in % : 99.352
number of unique conformers for further calc 3
list of relative energies saved as "crest.energies"
-----------------
Wall Time Summary
-----------------
CREGEN wall time : 0h : 0m : 0s
--------------------
Overall wall time : 0h : 0m : 0s
CREST terminated normally.
I also ran the same -nci job with a larger 1+ guest@CB8 complex (2 components) and it stops at the same place after performing hessian calcs on 26 ensemble structures:
writing TMPCONF* Dirs from file "crest_conformers.xyz" ... done.
---------------------------------------
Hessian calculations for all conformers
---------------------------------------
Performing calculations for 26 structures ...
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
done.
HOWEVER this time the cregen job incorrectly calculates the thermo data. Note that only one (not two) fragments are detected, and all 26 structures are removed from the ensemble as 'clashes' :(
Command line input:
> crest [email protected] -chrg 1 --cregen PROP/crest_property.xyz
-chrg 1
--cregen : CREGEN standalone usage. Sorting file <PROP/crest_property.xyz>
=============================
# threads = 12
=============================
Using only the cregen sorting routine.
input file name : PROP/crest_property.xyz
output file name : PROP/crest_property.xyz.sorted
number of atoms : 171
number of points on xyz files : 26
RMSD threshold : 0.1250
Bconst threshold : 0.0100
population threshold : 0.0500
conformer energy window /kcal : 6.0000
# fragment in coord : 1
number of removed clashes : 26
# bonds in reference structure : 198
number of reliable points : 0
reference state Etot : 1.158413105592492E-310
running RMSDs...
done.
number of doubles removed by rot/RMSD : 0
total number unique points considered further : 0
Erel/kcal Etot weight/tot conformer set degen origin
T /K : 298.15
E lowest : 0.00000
ensemble average energy (kcal) : 0.000
ensemble entropy (J/mol K, cal/mol K) : 0.000 0.000
ensemble free energy (kcal/mol) : 0.000
population of lowest in % : 0.000
number of unique conformers for further calc 0
list of relative energies saved as "crest.energies"
-----------------
Wall Time Summary
-----------------
CREGEN wall time : 0h : 0m : 0s
--------------------
Overall wall time : 0h : 0m : 0s
CREST terminated normally.
If you want to add some debugging checkpoints I'd be happy to run these again if it helps to locate the problem/bug.
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commented on June 4, 2024
The new 2.11 release (with xtb 6.3.3) appears to have fixed this problem, so closing this now.
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