internal error inside getieeab
jbarrozom opened this issue · 20 comments
After successfully running the initial ground state trajectory, I get this error when I try to generate the fragmentation runs:
preparing the IEE distribution ...
internal error inside getieeab
A smaller system of the same kind ran without any issue... Should I increase the ieeatm? Thank your for your assistance.
Best,
Jorge
@jbarrozom all input files plz.
@jbarrozom all input files plz.
I used the coord file (attached as coord.txt) with the default input parameters, no qcxms.in
Hi, at what point do you get this error? Can you send the erroneous output file as well?
Nevertheless, I see the two issues here:
- the molecule is pretty large, so the default IEE/atm value is probably not the best fitting for this type of molecule. I would increase both,
ieeatmandeimp0, as you probably need more energy distributed among the atoms. Maybe the latter first. - I have no experience with Dy atoms in a molecule, but xTB should be parametrized for it. I wonder if the atoms require more IEE anyways.
Hi, at what point do you get this error? Can you send the erroneous output file as well? Nevertheless, I see the two issues here:
- the molecule is pretty large, so the default IEE/atm value is probably not the best fitting for this type of molecule. I would increase both,
ieeatmandeimp0, as you probably need more energy distributed among the atoms. Maybe the latter first.- I have no experience with Dy atoms in a molecule, but xTB should be parametrized for it. I wonder if the atoms require more IEE anyways.
Yeah, I've done some somewhat smaller systems containing Dy atoms before with no issues. I can't use the plotms cause there's no Dy defined there; but I can plot the MS from the .res files though. I'll give it a try increasing the ieeatm and eimp0 though.
Thanks!
Did it work after increasing the parameters?
For Dy, maybe @gorges97 could implement it, if it would be something you really would like to have in PlotMS.
Did it work after increasing the parameters?
For Dy, maybe @gorges97 could implement it, if it would be something you really would like to have in PlotMS.
No luck with eimp0=100 and ieeatm=1.20; right now, I'm trying eimp0=200 and ieeatm=2.00
eimp0=100 and ieeatm 0.8 works, for example. (The more you increase ieeatm, the more you have to increase eimp0 to get the Poisson distribution converged.)
As for the isotopic masses in Plotms, I will add all elements up to Z=86 for the sake of completeness. Since xTB is parameterised for everything up to that point, missing isotopic masses should not be the problem.
eimp0=100 and ieeatm 0.8 works, for example. (The more you increase ieeatm, the more you have to increase eimp0 to get the Poisson distribution converged.) As for the isotopic masses in Plotms, I will add all elements up to Z=86 for the sake of completeness. Since xTB is parameterised for everything up to that point, missing isotopic masses should not be the problem.
Yeah, I got the same error with eimp0=100 adn ieeatm=1.20. Hopefully, eimp0=200 and ieeatm=2.00 will work. It's strange since all the output files seem to have everything in place.
It would be great to have all the xtb-available elements in plotms!
eimp0=200 and ieeatm=2.00 does not work, but eimp0=210 does for ieeatm=2.00. However, ieeatm=2.00 is probably way too much energy. By the way, you can start from the same ground state trajectory to try new energy settings, you just need the file qcxms.gs in the directory. You don't need to create a new ground state trajectory for this.
eimp0=200 and ieeatm=2.00 does not work, but eimp0=210 does for ieeatm=2.00. However, ieeatm=2.00 is probably way too much energy. By the way, you can start from the same ground state trajectory to try new energy settings, you just need the file qcxms.gs in the directory. You don't need to create a new ground state trajectory for this.
But if I try different energy settings to generate the fragmentation runs (with the qcxms.gs in the directory), the output file is not taking them into account. This is the output so far for eimp0=210 does for ieeatm=2.00:
************************************************************
Mode: Electron Impact (EI)
************************************************************
----- Internal program parameters -----
QC Program : xTB
QC Level : GFN2-xTB
Dispersion : D4
MO spectrum with : xTB
M+ Ion charge(charge) : 1
total traj. (ntraj) : 2300
time steps (tstep) : 0.50 fs
sim. time / MD (tmax) : 5.00 ps
Initial temp. (tinit) : 500.00 K
------------ EI settings -----------
E(e-impact) (eimp0) : 70.00 eV
Iee/atom (ieeatm) : 0.60 eV/atom
relax. time (trelax) : 2000.00 fs
--------------------------------------------
qc path /usr/local/bin/
--------------------------------------------
xtbhome directory ~/.XTBPARAM/
--------------------------------------------
reading qcxms.gs ...
--- Checking QC method for ions ---
initializing GFN2-xTB ...
initialization successful!
energy = -146.96771
charge = 1
mult = 2
etemp = 5000.0
--- QC method okay ---
*******************************************
generating randomized ensemble
*******************************************
reading inital coord/velo from qcxms.gs ...
doing XTB2 for MO spectrum for M ...
XTB-SCC levels (eV):
M alpha/beta -19.41 -19.36 -19.26 -19.20 -19.12 -19.06 -18.81 -18.48 -18.35 -18.28
M alpha/beta -18.25 -18.22 -18.18 -18.12 -16.97 -16.94 -16.81 -16.79 -16.69 -16.69
M alpha/beta -16.65 -16.63 -16.58 -16.56 -16.45 -16.44 -16.36 -16.34 -16.28 -16.27
M alpha/beta -16.14 -16.14 -15.83 -15.72 -15.66 -15.48 -15.33 -15.26 -15.24 -15.20
M alpha/beta -15.01 -14.96 -14.94 -14.71 -14.68 -14.62 -14.29 -14.17 -14.11 -14.08
M alpha/beta -14.06 -14.05 -13.97 -13.96 -13.93 -13.90 -13.89 -13.86 -13.85 -13.84
M alpha/beta -13.82 -13.82 -13.75 -13.75 -13.65 -13.65 -13.64 -13.59 -13.53 -13.53
M alpha/beta -13.46 -13.45 -13.38 -13.35 -13.21 -13.19 -13.09 -13.09 -12.73 -12.72
M alpha/beta -12.69 -12.60 -12.58 -12.57 -12.57 -12.57 -12.45 -12.44 -12.39 -12.37
M alpha/beta -12.34 -12.32 -12.29 -12.26 -12.25 -12.24 -12.19 -12.17 -12.16 -12.14
M alpha/beta -12.13 -12.11 -12.10 -12.09 -12.09 -12.05 -11.98 -11.97 -11.88 -11.77
M alpha/beta -11.02 -10.88 -10.69 -10.69 -10.55 -10.53 -10.01 -10.00 -9.97 -9.96
M alpha/beta -9.82 -9.81 -9.80 -9.75 -9.74 -9.73 -9.61 -9.60
MO localization degree (number of centers)
alpha/beta 14.20 19.30 15.90 11.97 14.19 13.24 16.96 13.93 13.80 17.20
alpha/beta 17.30 17.73 16.23 12.03 31.94 21.63 23.88 15.42 37.34 23.36
alpha/beta 29.56 21.72 32.02 21.59 11.32 11.12 24.45 25.21 14.35 13.99
alpha/beta 12.91 13.17 36.06 46.73 39.70 34.83 36.12 43.50 30.30 36.93
alpha/beta 37.76 33.66 36.19 22.77 39.65 24.87 41.31 37.67 31.26 37.05
alpha/beta 26.18 25.73 28.02 37.82 25.68 30.94 42.33 37.58 39.47 49.69
alpha/beta 23.00 20.98 36.14 34.40 16.16 15.75 28.75 34.35 33.89 28.53
alpha/beta 19.42 23.43 26.74 27.25 33.17 42.86 21.59 20.24 25.48 14.64
alpha/beta 32.04 17.93 13.22 12.12 35.56 26.55 15.76 16.79 37.29 49.50
alpha/beta 28.48 45.98 43.14 46.40 12.92 14.21 47.33 30.01 30.28 38.43
alpha/beta 27.79 46.69 37.96 36.50 17.29 17.96 19.24 22.33 6.91 3.90
alpha/beta 22.39 11.60 10.51 14.04 12.46 9.71 16.55 14.44 14.67 15.44
alpha/beta 6.74 5.54 6.70 10.15 4.75 4.68 6.24 6.98
preparing the IEE distribution ...
internal error inside getieeab
That's strange. But if you re-calculate the ground state trajectory it works? Could you provide your qcxms.in file?
You have to be careful increasing the iee to unrealistically high values. Lets see, you got 92 atoms with 70 eV, you would have a iee/atom of ~0.78 eV/atom. Did you try to increase the ieeatm to 0.8 without the eimp0? Alternatively, try 100 eV with 1 or 1.1 iee/atm. Does it still fail?
That's strange. But if you re-calculate the ground state trajectory it works? Could you provide your qcxms.in file?
Well, check again what is written there. Isn't there some kind of MO file, that stores this information? (sorry, already some time ago that I used it)
That's strange. But if you re-calculate the ground state trajectory it works? Could you provide your qcxms.in file?
This is my entire qcxms.in file, since I'm just moving these parameters, I kept everything else as default:
eimp0 200
ieeatm 2.00
I ran a quick test with methane, if I include this qcxms.in when computing the ground I do get these parameters:
----- Internal program parameters -----
QC Program : xTB
QC Level : GFN2-xTB
Dispersion : D4
MO spectrum with : xTB
M+ Ion charge(charge) : 1
total traj. (ntraj) : 125
time steps (tstep) : 0.50 fs
sim. time / MD (tmax) : 5.00 ps
Initial temp. (tinit) : 500.00 K
------------ EI settings -----------
E(e-impact) (eimp0) : 200.00 eV
Iee/atom (ieeatm) : 2.00 eV/atom
relax. time (trelax) : 2000.00 fs
You have to be careful increasing the iee to unrealistically high values. Lets see, you got 92 atoms with 70 eV, you would have a iee/atom of ~0.78 eV/atom. Did you try to increase the
ieeatmto 0.8 without theeimp0? Alternatively, try 100 eV with 1 or 1.1 iee/atm. Does it still fail?
I'll give it a try with those parameters, thanks!!
0.8 with default eimp0 won't work. As I said, if you increase ieeatm you have to increase eimp0 even more. If ieeatm=0.6 with eimp0=70 doesn't work, ieeatm=0.8 with eimp0=70 certainly doesn't work!
Right now, I'm running the ground state with eimp0 200 and ieeatm 2.00, and it could be too much energy, but if it can get the fragmentation runs, then I can move the energy down.
On an update: I was able to generate the fragmentation runs by changing to a gaussian IEE distribution.
On the other hand, I wasn't copying the qcxms.in in the working directory, that's why I had to re-run the ground state for every new setting I was trying.
Thank you!
Great, that is also a possible solution to this problem.
Ok, very good, so everything works as it should after all and no energy distribution information is written from the ground state trajectory calculation.
By the way, I have just published plotms version 6.2, which now contains the isotopes of all stable elements up to bismuth.
Great, that is also a possible solution to this problem. Ok, very good, so everything works as it should after all and no energy distribution information is written from the ground state trajectory calculation. By the way, I have just published plotms version 6.2, which now contains the isotopes of all stable elements up to bismuth.
Awesome!