[CP2K-user] [CP2K:21197] Re: Langevin simulation error in CP2K

[Marcella Iannuzzi]

HI Zhang Yichen

There should be no commas in the lists of atoms
LIST 1..282, 377..517
Regards
Marcella



On Saturday, February 22, 2025 at 7:15:11 AM UTC+1 zhangyi... at gmail.com 
wrote:

> Dear CP2K Community,
>
> I am encountering an error while running a Langevin simulation in CP2K. I 
> would appreciate your assistance in resolving this issue.
>
> *Input File:* 
>
> &GLOBAL
>   PROJECT cp2k
>   PRINT_LEVEL LOW
>   RUN_TYPE MD
> &END GLOBAL
>
> &MOTION
>   &MD
>     ENSEMBLE LANGEVIN
>     STEPS 200
>     TIMESTEP 1
>     TEMPERATURE 298.15
>       &LANGEVIN
>         GAMMA 0.005
>         NOISY_GAMMA 0.0001
>       &END LANGEVIN
>       &THERMAL_REGION
>         DO_LANGEVIN_DEFAULT F 
>         &DEFINE_REGION
>           TEMPERATURE 298.15
>           DO_LANGEVIN T
>           LIST 1..282, 377..517
>           NOISY_GAMMA_REGION 1E-4
>         &END DEFINE_REGION
>         &DEFINE_REGION
>           TEMPERATURE 298.15
>           DO_LANGEVIN F
>           LIST 283..376, 518
>           NOISY_GAMMA_REGION 1E-6
>         &END DEFINE_REGION
>       &END THERMAL_REGION
>   &END MD
>   &GEO_OPT
>     TYPE MINIMIZATION #Search for minimum
>     KEEP_SPACE_GROUP F #If T, then space group will be detected and 
> preserved
>     OPTIMIZER LBFGS #Can also be CG (more robust for difficult cases) or 
> BFGS
>     &LBFGS
>       TRUST_RADIUS 0.2 #Trust radius (maximum stepsize) in Angstrom
>       MAX_H_RANK 5 #Larger values (e.g. 30) will accelerate convergence 
> behaviour at the cost of a larger memory consumption
>     &END LBFGS
>     MAX_ITER 500 #Maximum number of geometry optimization
>     MAX_DR 3E-3 #Maximum geometry change
>     RMS_DR 1.5E-3 #RMS geometry change
>     MAX_FORCE 6E-4 #Maximum force
>     RMS_FORCE 3E-4 #RMS force
>   &END GEO_OPT
>   &PRINT
>     &TRAJECTORY
>       FORMAT xyz
>       &EACH
>         MD 1
>       &END EACH
>     &END TRAJECTORY
>     &VELOCITIES
>       &EACH
>         MD 1
>       &END EACH
>     &END VELOCITIES
>     &RESTART
>       BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means 
> never
>     &END RESTART
>     &RESTART_HISTORY
>      &EACH
>       MD 500
>      &END EACH
>     &END RESTART_HISTORY
>   &END PRINT
> &END MOTION
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &SUBSYS
>     &CELL
>       ABC 17.0434 14.7600 20.0000
>       ALPHA_BETA_GAMMA 90 90 90 
>       PERIODIC XYZ #Direction(s) of applied PBC (geometry aspect)
>     &END CELL
>     &COORD
>       @INCLUDE 'coord.inc'
>     &END COORD
>     &KIND Fe
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q16
>     &END KIND
>     &KIND O
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>     &KIND C
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>     &KIND H
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q1
>       MASS 2.0
>     &END KIND
>     &KIND N
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q5
>     &END KIND
>   &END SUBSYS
>
>   &DFT
>     UKS T  
>     @SET DATAPATH /public/home/chenyicong/cp2k_data
>     POTENTIAL_FILE_NAME ${DATAPATH}/GTH_POTENTIALS  
>     BASIS_SET_FILE_NAME ${DATAPATH}/BASIS_MOLOPT 
>     WFN_RESTART_FILE_NAME ./RESTART.wfn
>     CHARGE    0 #Net charge
>     MULTIPLICITY    1 #Spin multiplicity
>     &QS
>       EXTRAPOLATION_ORDER 0#need test 0 1 2 3
>       EPS_PGF_ORB 1.0E-6
>       EXTRAPOLATION ASPC
>       EPS_DEFAULT 1.0E-12 #Set all EPS_xxx to values such that the energy 
> will be correct up to this value
>     &END QS
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>       &XC_GRID
>        XC_SMOOTH_RHO NN10
>        XC_DERIV SPLINE2_SMOOTH
>       &END XC_GRID
>        &VDW_POTENTIAL
>         POTENTIAL_TYPE PAIR_POTENTIAL
>         &PAIR_POTENTIAL
>           PARAMETER_FILE_NAME ${DATAPATH}/dftd3.dat
>           TYPE DFTD3
>           REFERENCE_FUNCTIONAL PBE
>           R_CUTOFF 10.
>         &END PAIR_POTENTIAL
>       &END VDW_POTENTIAL
>     &END XC
>     &MGRID
>       CUTOFF 400
>       NGRIDS 20
>       REL_CUTOFF 40
>     &END MGRID
>     &SCF
>       SCF_GUESS RESTART
>       MAX_SCF 100 #Maximum number of steps of inner SCF
>       EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF
>       MAX_SCF_HISTORY 5
>       &OT
>         PRECONDITIONER FULL_SINGLE_INVERSE 
> #FULL_KINETIC&FULL_SINGLE_INVERSE is also worth to try. FULL_ALL is better 
> but quite expensive for large system
>         MINIMIZER BROYDEN #CG is worth to consider in difficult cases
>         BROYDEN_BETA 0.9
>         BROYDEN_SIGMA 0.1
>         LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default. 
> 3PNT is more expensive but may be better. GOLD is best but very expensive
>       &END OT
>       &OUTER_SCF
>         MAX_SCF 20 #Maximum number of steps of outer SCF
>         EPS_SCF 1.0E-05 #Convergence threshold of outer SCF
>       &END OUTER_SCF
>       &MIXING ON
>        ALPHA 0.1
>        BETA 0.5
>       &END MIXING
>       &PRINT
>         &RESTART #Note: Use "&RESTART OFF" can prevent generating .wfn file
>           FILENAME =RESTART.wfn
>           BACKUP_COPIES 0 #Maximum number of backup copies of wfn file. 0 
> means never
>         &END RESTART
>       &END PRINT
>     &END SCF
>   &END DFT
>
>   &PRINT
>     &FORCES ON
>     &END FORCES
>   &END PRINT
> &END FORCE_EVAL
>
> *Error Message:* 
>
> [image: WeChat21f164d341cdf7c90fcd0053d7821503.jpg]
>
> Thank you in advance for your help.
>
> Best regards,
>
> Zhang Yichen
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cp2k/b09abbee-b079-42a5-bbfc-fd948ae27b82n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20250222/ae6bdf05/attachment.htm>