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NaN elec energy when running crystal simulation
#37903 06/01/20 02:58 AM
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Hello,

I had a very strange error when trying to simulate 8 unit cells of monoclinic crystal type. I got NaN elec energy after running an ener command. All other terms seem fine. Simulation then ceased in following minimization step. The initial structure was obtained from crystal identity transformation from an unit cell which was created from a single asymmetric unit. I got NPT simulation of both unit cell and asymmetric unit running without issue. When it turns to the 8 unit cells, I doubled the box length in a b and c direction. That's the only difference in input. Any hints are very appreciated.

Thank you.

///////////////////
.....
crystal define Monoclinic 21.678 26.698 9.908 90 91.31 90
crystal build noper 0 cutoff 25
image BYSEgments xcen 0.0 ycen 0.0 zcen 0.0 select all end
update inbfrq -1 imgfrq -1 ihbfrq 0 -
ewald pmewald kappa 0.34 fftx 32 ffty 32 fftz 32 order 6 lrc -
@eatom @etrun @vatom @vtrun cutnb 16 ctonnb 10 ctofnb 12 -
cutim 16
ener (issue occurs)
....
////////////////

ENER> 0 NaN 0.00000 NaN
ENER INTERN> 2013.77437 433.97566 93.57481 1231.67113 0.00000
ENER EXTERN> -52.75399 NaN 0.00000 0.00000 0.00000
ENER IMAGES> -241.68327 -220.10314 0.00000 0.00000 0.00000
ENER EWALD> 41.12251-127697.21203 127425.59880 0.00000 0.00000
ENER LRCor> -9.61290 -19.22339

Last edited by Allen_123; 06/01/20 06:33 AM.
Re: NaN elec energy when running crystal simulation
Allen_123 #37904 06/01/20 03:21 AM
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rmv Online Content
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What other steps have you taken? Did you create an 8-fold larger psf, and then replicate the coordinates seven times? Did you change the Cartesian placement of the atoms in any way?


Rick Venable
computational chemist

Re: NaN elec energy when running crystal simulation
rmv #37905 06/01/20 06:37 AM
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Yes, exactly as you said. The setup is as following:

/////////
!read psf and crd of one unit cell
crystal define Monoclinic 10.839 13.349 4.954 90 91.31 90 ! dimension of one unitcell
crystal build noper 0 cutoff 13
GENErate B DUPLicate A setup
GENErate C DUPLicate A setup
GENErate D DUPLicate A setup
GENErate E DUPLicate A setup
GENErate F DUPLicate A setup
GENErate G DUPLicate A setup
GENErate H DUPLicate A setup


COOR duplicate sele segid A end sele segid B end
coor oper C027 sele segid B end


COOR duplicate sele segid A end sele segid C end
coor oper C028 sele segid C end


COOR duplicate sele segid A end sele segid D end
coor oper C031 sele segid D end


COOR duplicate sele segid A end sele segid E end
coor oper C032 sele segid E end


COOR duplicate sele segid A end sele segid F end
coor oper C042 sele segid F end

COOR duplicate sele segid A end sele segid G end
coor oper C043 sele segid G end


COOR duplicate sele segid A end sele segid H end
coor oper C046 sele segid H end

!then create psf and crd for eight cells

/////////////////////////////////

Last edited by Allen_123; 06/01/20 06:51 AM.
Re: NaN elec energy when running crystal simulation
Allen_123 #37906 06/01/20 04:50 PM
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rmv Online Content
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Still not enough information to make a suggestion other than carefully reviewing your output logs and coordinates.


Rick Venable
computational chemist

Re: NaN elec energy when running crystal simulation
Allen_123 #37907 06/02/20 07:35 AM
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You can add the duplicates one at a time, and each time see if you get the electrostatic NaN.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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