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11
General / Re: Warning: Reinsertion used on the charged ions
« Last post by David Dubbeldam on January 07, 2021, 08:02:11 PM »
The reason for the warning is that using CBMC with regrow is not advisable when the molecule has a net charge. The energies could become why to small/large leading to under/overflow.
It is better than for cations to use 'random translation'.

If the net-charge changes it can be because the adsorbate has a (small) net charge. With inserting adsorbates it will then grow in magnitude.
12
Input files and parameters / Re: Change input file when restart
« Last post by David Dubbeldam on January 07, 2021, 07:58:34 PM »
Using the 'binary' file, the simulation should immediately end, since it was already finished. There is no wya to extend a binary restart.
The other form of restart just use the initial positions written as output from the previous run.
The positions are written to 'Restart', while reading is from 'RestartInitial' to avoid overwriting these.
To restart, copy 'Restart' to 'RestartInitial'.
If results are different, then you did not equilibrate long enough.
13
Hi,
I ran a full  MC simulation consisting of 10K init, 50K equil and 200K production runs.
I then tried to run a new simulation but using the binary file from the a.m. simulation as basis. it did work ( there was a Restart folder which I renamed to restartInit first and then ran a new short simulation with restart option ON in simulation.input and 0 init, 1000 equil and 50000 production. But I am getting very different energy values ( about 3 times). Where did I get it wrong?

ii. Also  I was wondering if it is possible to make a run in progress with 70K equil previously set in input file to extend to a higher cycle numebr say , 150K before production run has started ?
many thanks
Mas
14
Input files and parameters / Re: Change input file when restart
« Last post by mhaeri on January 04, 2021, 10:05:23 PM »
Hi,
I ran a full  MC simulation consisting of 10K init, 50K equil and 200K production runs.
I then tried to run a new simulation but using the binary file from the a.m. simulation as basis. it did work ( there was a Restart folder which I renamed to restartInit first and then ran a new short simulation with restart option ON in simulation.input and 0 init, 1000 equil and 50000 production. But I am getting very different energy values ( about 3 times). Where did I get it wrong?

ii. Also  I was wondering if it is possible to make a run in progress with 70K equil previously set in input file to extend to a higher cycle numebr say , 150K before production run has started ?
many thanks
Mas
15
Bug reports / Re: Charge Equilibration leads to Segmentation Fault
« Last post by neumannrf on January 04, 2021, 05:29:24 PM »
Happy New Year, David!

I investigated the encoding hypothesis you raised, but found no explanation so far. The (attached) TER.cif file from https://asia.iza-structure.org/IZA-SC/cif/TER.cif seems to be encoded in plain ASCII.
Code: [Select]
rneumann@linux:$>  file -i TER.cif
TER.cif: text/plain; charset=us-ascii

rneumann@macos:$>  file -I TER.cif
TER.cif: text/plain; charset=us-ascii

Also, if I open it in binary mode with vim -b TER.cif, I don't find a sneaky ^M anywhere. Everything seems pretty normal. In any case, I tried converting the encoding from ASCII to UTF-8 using the iconv -f ASCII -t UTF-8 TER.cif > TER-utf8.cif command but got the same behaviour when simulating TER-utf8.cif. The problem does not seem to be in the part that reads the CIF file, because I even get a End reading cif-file success message minutes before the crash happens.


The other thing you suggested, though, gave rise to much more interesting results. If I run either
  • UnitCells  3 2 2 + ChargeFromChargeEquilibration   no
  • UnitCells  1 1 1 + ChargeFromChargeEquilibration   yes
the calculation runs perfectly to the end.

Could there be an effect that only manifests itself when a combination of large supercell + charge equilibration is present?
16
General / Warning: Reinsertion used on the charged ions
« Last post by Monica_Gao on December 27, 2020, 09:14:37 AM »
Dear professor David,
   Recently, I find when I use the instruction: regrowprobability, the output result will warn that "Reinsertion used on the charged ions", but I have checked the molecular file, and there is no wrong about them. Stranger is that, the total charges of adsorbates will change with the cycle.


[Init] Current cycle: 0 out of 80000
========================================================================================================

Net charge: -4.22752e-14 (F: -4.22752e-14, A: 0, C: 0)

WARNING: REINSERTION MOVE USED ON CHARGED IONS (IF POSSIBLE, CHANGE TO RANDOM TRANSLATION MOVE TO AVOID NUMERICAL PROBLEMS)

[Init] Current cycle: 20000 out of 80000
========================================================================================================

Net charge: 1.446 (F: -4.22752e-14, A: 1.446, C: 0)

Could you please give me some advice, thank you very much!

Best regard
Monica Gao
17
Input files and parameters / Re: Error in connectivity
« Last post by Monica_Gao on December 27, 2020, 08:46:41 AM »
Dear professor David,
Thank you very much. And Merry Chrisma  ;D
18
General / Re: Issue with ExtraFrameworkMolecule
« Last post by Kajum Safiullin on December 25, 2020, 11:41:41 AM »
Thank you for the reply, I'll try to recompile it.
19
Input files and parameters / Re: Error in connectivity
« Last post by David Dubbeldam on December 23, 2020, 09:23:51 PM »
Check the manual and examples. There are explicit examples for mixtures and adsorption mixtures,
for example:
examples/Basic/MC_BinaryMixture_in_Box
examples/Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1
20
General / Re: How to eliminate the boundary effect in GEMC simulations?
« Last post by David Dubbeldam on December 23, 2020, 09:20:53 PM »
Do you mean that you want to simulate adsorption on the outside of the zeolite?
Because using the grand-canonical approach only the adsorbed phase inside the framework is computed.

I have no experience with adsorption on the external surface of a zeolite.
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