[CPMD-list] fail to read RESTART?
Lan-Feng Yuan
yuanlf at ustc.edu.cn
Tue Dec 19 23:49:50 CET 2006
Dear Nisanth,
Thank you very much, your suggestion is correct! What seems strange is that with
VELOCITES and NOSEP in RESTART keyword the program runs just fine in many other
jobs, so this is an unpredictable problem ... Without reading VELOCITIES, the
system starts with the target temperature, which is a bad thing as I understand.
Therefore, maybe we should use QUENCH IONS, ELECTRONS to make the initial
velocities zero. Thanks again!
Lan-Feng
In your mail:
>From: Nisanth Nair <nisanth.nair at theochem.ruhr-uni-bochum.de>
>Reply-To:
>To: Lan-Feng Yuan <yuanlf at ustc.edu.cn>
>Subject: Re: [CPMD-list] fail to read RESTART?
>Date:Tue, 19 Dec 2006 23:05:32 +0100 (CET)
>
>Hi Lan,
>
> You are trying to read some information which is not in the
> restart file. Don't restart the velocities and Nose information from a
> restart file after the wavefunction or geometry optimization!
>
> With best regards,
> Nisanth
>
>
> On Wed, 20 Dec 2006, Lan-Feng Yuan wrote:
>
> > Dear CPMD people,
> >
> > Sometimes I meet strange cases where a RESTART file cannot be read into a
MD
> > run. For example, for the molecule H2, a RESTART file is generated by:
> >
> > &CPMD
> > CENTER MOLECULE
> > ISOLATED MOLECULE
> > OPTIMIZE WAVEFUNCTION
> > CONVERGENCE ORBITALS
> > 1.D-8
> > &END
> >
> > &DFT
> > FUNCTIONAL PBE
> > &END
> >
> > &SYSTEM
> > ANGSTROM
> > SYMMETRY
> > 1
> > CELL
> > 5.000 1. 1. 0.0 0.0 0.0
> > CUTOFF
> > 80.00
> > &END
> >
> > &ATOMS
> > ISOTOPE
> > 1.007825
> > *H_MT_PBE.psp KLEINMAN-BYLANDER
> > LMAX=S
> > 2
> > 2.290887532260 2.270887532267 2.280887532298
> > 2.719112467740 2.739112467733 2.711312467702
> > &END
> >
> > Then I try to read it to start a MD simulation:
> >
> > &CPMD
> > CENTER MOLECULE
> > MOLECULAR DYNAMICS CP
> > CONVERGENCE ORBITALS
> > 1.D-7
> > EMASS
> > 100
> > TIMESTEP
> > 1.5
> > NOSE IONS MASSIVE
> > 300.0 5000.0
> > NOSE PARAMETER
> > 20 0 0 6. 625 4
> > MAXSTEP
> > 20000
> > TRAJECTORY XYZ
> > RESTART COORDINATES CELL WAVEFUNCTIONS VELOCITIES LATEST NOSEP
> > STORE
> > 500
> > &END
> >
> > &DFT
> > NEWCODE
> > FUNCTIONAL PBE
> > &END
> >
> > &SYSTEM
> > ANGSTROM
> > SYMMETRY
> > 1
> > CELL
> > 5.000 1. 1. 0.0 0.0 0.0
> > CUTOFF
> > 80.00
> > &END
> >
> > But the program outputs a lot of "NaN":
> >
> > CPU TIME FOR INITIALIZATION: 0.44 SECONDS
> >
> > ATOM COORDINATES GRADIENTS (-FORCES)
> > 1 H 4.3292 4.2914 4.3103 NaN NaN NaN
> > 2 H 5.1384 5.1762 5.1236 NaN NaN NaN
> >
> > TOTAL INTEGRATED ELECTRONIC DENSITY
> > IN G-SPACE = Infinity
> > IN R-SPACE = NaN
> >
> > (K+E1+L+N+X) TOTAL ENERGY = NaN A.U.
> > (K) KINETIC ENERGY = NaN A.U.
> > (E1=A-S+R) ELECTROSTATIC ENERGY = NaN A.U.
> > (S) ESELF = 0.66490380 A.U.
> > (R) ESR = 0.15685511 A.U.
> > (L) LOCAL PSEUDOPOTENTIAL ENERGY = NaN A.U.
> > (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
> > (X) EXCHANGE-CORRELATION ENERGY = 0.00000000 A.U.
> > GRADIENT CORRECTION ENERGY = 0.00000000 A.U.
> >
> > NFI EKINC TEMPP EKS ECLASSIC EHAM
DIS
> > TCPU
> > 1 NaN NaN NaN NaN NaN
0.204E-11
> > 0.47
> > 2 NaN NaN NaN NaN NaN NaN
> > 0.40
> > 3 NaN NaN NaN NaN NaN NaN
> > 0.43
> > 4 NaN NaN NaN NaN NaN NaN
> > 0.41
> > 5 NaN NaN NaN NaN NaN NaN
> > 0.40
> > 6 NaN NaN NaN NaN NaN NaN
> > 0.41
> >
> > In some other cases of the same problem, I can make the RESTART read
correctly
> > by adjusting some parameters (like Nose frequency or number of CPUs; funny,
isn't
> > it?). However, for this H2 thing, I get no luck. This same trouble occurs in
both
> > 3.10 and 3.11.
> >
> > Did anyone see this problem before? Your help will be greatly appreciated.
Thank
> > you very much!
> >
> > Lan-Feng
> >
> >
> >
> >
> > ------------------------------
> > -------------------------------------------------
> > Dr. Lan-Feng Yuan,
> > Associate Professor,
> > Hefei National Laboratory for Physical Sciences at the Microscale,
> > University of Science and Technology of China,
> > Hefei, Anhui 230026, People's Republic of China
> > Email: yuanlf at ustc.edu.cn
> > Telephone: 86-551-3600994
> > -------------------------------------------------
> > _______________________________________________
> > CPMD-list mailing list
> > CPMD-list at cpmd.org
> > http://cpmd.org/mailman/listinfo/cpmd-list
> >
>
> ===========================================================================
> Dr. Nisanth N. Nair
> Lehrstuhl fuer Theoretische Chemie Tel: ++49 (0)234 32 22121
> Ruhr-Universitaet Bochum Fax: ++49 (0)234 32 14045
> Universitaetstrasse 150
> D-44801 Bochum, Germany
> Email: nisanth.nair at theochem.ruhr-uni-bochum.de
> Web : http://www.theochem.ruhr-uni-bochum.de
> ===========================================================================
>
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