Atoms are not relaxing, but successful optimization
Nathaniel Swenson
nate... at gmail.com
Wed Mar 21 18:45:47 UTC 2012
Hello,
My greatest apologies if you have already checked this, but this is a
simple point of clarification:
The cell_d-pos-1.xyz file typically should contain not just ONE set of
coordinates, but it should have sets of coordinates from ALL the
geometry optimization steps, all in one file. Typically, the first
set of coordinates that appear in this file are your input
coordinates, so if you are simply opening this file with a
visualization program, this could explain why you are only getting
your input coordinates back. On the contrary, the last set of
coordinates in the file should be your optimized coordinates.
How many sets of coordinates are showing up in your cell_d-pos-1.xyz
file?
Best wishes,
Nathaniel Swenson
Northwestern University
On Mar 21, 12:12 pm, Samuel Lamphier <samuell... at gmail.com> wrote:
> Hello all, I am modeling cerium oxide nano particles. I have prepared
> input file with high cutoffs, however, I have had good luck with
> optimizations. Then I discovered a problem, my atoms are not relaxing,
> is there something I am doing incorrectly?
>
> &GLOBAL
> PRINT_LEVEL LOW
> PROJECT_NAME cell_d
> RUN_TYPE CELL_OPT
> FLUSH_SHOULD_FLUSH T
> &END GLOBAL
> &MOTION
> &GEO_OPT
> TYPE MINIMIZATION
> OPTIMIZER BFGS
> MAX_ITER 5000
> MAX_DR 2.9999999999999997E-05
> MAX_FORCE 5.0000000000000003E-06
> RMS_DR 1.4999999999999999E-05
> RMS_FORCE 5.0000000000000001E-06
> STEP_START_VAL 1
> &PRINT
> &PROGRAM_RUN_INFO
> &END PROGRAM_RUN_INFO
> &END PRINT
> &END GEO_OPT
> &CELL_OPT
> OPTIMIZER CG
> MAX_ITER 3000
> MAX_DR 3.0000000000000001E-05
> MAX_FORCE 5.0000000000000000E-06
> RMS_DR 1.5000000000000000E-05
> RMS_FORCE 2.9999999999999997E-06
> STEP_START_VAL 1
> TYPE GEO_OPT
> PRESSURE_TOLERANCE 1.0000000000000000E-01
> &CG
> MAX_STEEP_STEPS 0
> RESTART_LIMIT 9.4999999999999996E-01
> &LINE_SEARCH
> TYPE 2PNT
> &END LINE_SEARCH
> &END CG
> &END CELL_OPT
> &END MOTION
> &FORCE_EVAL
> METHOD QS
> STRESS_TENSOR ANALYTICAL
> &DFT
> CHARGE 0
> PLUS_U_METHOD MULLIKEN
> &SCF
> MAX_SCF 1000
> EPS_SCF 9.9999999999999995E-08
> SCF_GUESS ATOMIC
> &OT T
> MINIMIZER DIIS
> PRECONDITIONER FULL_ALL
> ENERGY_GAP 1.0000000000000000E-03
> &END OT
> &OUTER_SCF T
> EPS_SCF 9.9999999999999995E-08
> &END OUTER_SCF
> &END SCF
> &QS
> EPS_DEFAULT 9.9999999999999998E-13
> &END QS
> &MGRID
> CUTOFF 3.0000000000000000E+02
> &END MGRID
> &XC
> DENSITY_CUTOFF 1.0000000000000000E-10
> GRADIENT_CUTOFF 1.0000000000000000E-10
> TAU_CUTOFF 1.0000000000000000E-10
> &XC_GRID
> XC_SMOOTH_RHO NONE
> XC_DERIV SPLINE2_SMOOTH
> &END XC_GRID
> &XC_FUNCTIONAL NO_SHORTCUT
> &PADE T
> &END PADE
> &END XC_FUNCTIONAL
> &END XC
> &PRINT
> &MO_CUBES SILENT
> STRIDE 1 1 1
> NLUMO 0
> NHOMO 1
> &EACH
> GEO_OPT 1
> &END EACH
> &END MO_CUBES
> &E_DENSITY_CUBE SILENT
> STRIDE 1 1 1
> &EACH
> GEO_OPT 1
> &END EACH
> &END E_DENSITY_CUBE
> &TOT_DENSITY_CUBE SILENT
> STRIDE 1 1 1
> &EACH
> GEO_OPT 1
> &END EACH
> &END TOT_DENSITY_CUBE
> &PDOS SILENT
> &EACH
> GEO_OPT 1
> &END EACH
> &END PDOS
> &MULLIKEN
> &EACH
> GEO_OPT 1
> &END EACH
> &END MULLIKEN
> &LOWDIN
> &EACH
> GEO_OPT 1
> &END EACH
> &END LOWDIN
> &DFT_CONTROL_PARAMETERS
> &END DFT_CONTROL_PARAMETERS
> &PLUS_U
> &END PLUS_U
> &END PRINT
> &END DFT
> &SUBSYS
> &CELL
> A 16.23402000 0.000000000 0.0000000000
> B 0.000000000 16.23402000 0.0000000000
> C 0.000000000 0.000000000 16.234020000
> PERIODIC XYZ
> &END CELL
> &COORD
> Ce 0.00000 14.88119 14.88119
> Ce 0.00000 14.88119 9.46985
> Ce 0.00000 14.88119 4.05851
> Ce 0.00000 9.46985 14.88119
> Ce 0.00000 9.46985 9.46985
> Ce 0.00000 9.46985 4.05851
> Ce 0.00000 4.05851 14.88119
> Ce 0.00000 4.05851 9.46985
> Ce 0.00000 4.05851 4.05851
> Ce 5.41134 14.88119 14.88119
> Ce 5.41134 14.88119 9.46985
> Ce 5.41134 14.88119 4.05851
> Ce 5.41134 9.46985 14.88119
> Ce 5.41134 9.46985 9.46985
> Ce 5.41134 9.46985 4.05851
> Ce 5.41134 4.05851 14.88119
> Ce 5.41134 4.05851 9.46985
> Ce 5.41134 4.05851 4.05851
> Ce 10.82268 14.88119 14.88119
> Ce 10.82268 14.88119 9.46985
> Ce 10.82268 14.88119 4.05851
> Ce 10.82268 9.46985 14.88119
> Ce 10.82268 9.46985 9.46985
> Ce 10.82268 9.46985 4.05851
> Ce 10.82268 4.05851 14.88119
> Ce 10.82268 4.05851 9.46985
> Ce 10.82268 4.05851 4.05851
> Ce 0.00000 12.17552 12.17552
> Ce 0.00000 12.17552 6.76418
> Ce 0.00000 12.17552 1.35284
> Ce 0.00000 6.76418 12.17552
> Ce 0.00000 6.76418 6.76418
> Ce 0.00000 6.76418 1.35284
> Ce 0.00000 1.35284 12.17552
> Ce 0.00000 1.35284 6.76418
> Ce 0.00000 1.35284 1.35284
> Ce 5.41134 12.17552 12.17552
> Ce 5.41134 12.17552 6.76418
> Ce 5.41134 12.17552 1.35284
> Ce 5.41134 6.76418 12.17552
> Ce 5.41134 6.76418 6.76418
> Ce 5.41134 6.76418 1.35284
> Ce 5.41134 1.35284 12.17552
> Ce 5.41134 1.35284 6.76418
> Ce 5.41134 1.35284 1.35284
> Ce 10.82268 12.17552 12.17552
> Ce 10.82268 12.17552 6.76418
> Ce 10.82268 12.17552 1.35284
> Ce 10.82268 6.76418 12.17552
> Ce 10.82268 6.76418 6.76418
> Ce 10.82268 6.76418 1.35284
> Ce 10.82268 1.35284 12.17552
> Ce 10.82268 1.35284 6.76418
> Ce 10.82268 1.35284 1.35284
> Ce 2.70567 12.17552 14.88119
> Ce 2.70567 12.17552 9.46985
> Ce 2.70567 12.17552 4.05851
> Ce 2.70567 6.76418 14.88119
> Ce 2.70567 6.76418 9.46985
> Ce 2.70567 6.76418 4.05851
> Ce 2.70567 1.35284 14.88119
> Ce 2.70567 1.35284 9.46985
> Ce 2.70567 1.35284 4.05851
> Ce 8.11701 12.17552 14.88119
> Ce 8.11701 12.17552 9.46985
> Ce 8.11701 12.17552 4.05851
> Ce 8.11701 6.76418 14.88119
> Ce 8.11701 6.76418 9.46985
> Ce 8.11701 6.76418 4.05851
> Ce 8.11701 1.35284 14.88119
> Ce 8.11701 1.35284 9.46985
> Ce 8.11701 1.35284 4.05851
> Ce 13.52835 12.17552 14.88119
> Ce 13.52835 12.17552 9.46985
> Ce 13.52835 12.17552 4.05851
> Ce 13.52835 6.76418 14.88119
> Ce 13.52835 6.76418 9.46985
> Ce 13.52835 6.76418 4.05851
> Ce 13.52835 1.35284 14.88119
> Ce 13.52835 1.35284 9.46985
> Ce 13.52835 1.35284 4.05851
> Ce 2.70567 14.88119 12.17552
> Ce 2.70567 14.88119 6.76418
> Ce 2.70567 14.88119 1.35284
> Ce 2.70567 9.46985 12.17552
> Ce 2.70567 9.46985 6.76418
> Ce 2.70567 9.46985 1.35284
> Ce 2.70567 4.05851 12.17552
> Ce 2.70567 4.05851 6.76418
> Ce 2.70567 4.05851 1.35284
> Ce 8.11701 14.88119 12.17552
> Ce 8.11701 14.88119 6.76418
> Ce 8.11701 14.88119 1.35284
> Ce 8.11701 9.46985 12.17552
> Ce 8.11701 9.46985 6.76418
> Ce 8.11701 9.46985 1.35284
> Ce 8.11701 4.05851 12.17552
> Ce 8.11701 4.05851 6.76418
> Ce 8.11701 4.05851 1.35284
> Ce 13.52835 14.88119 12.17552
> Ce 13.52835 14.88119 6.76418
> Ce 13.52835 14.88119 1.35284
> Ce 13.52835 9.46985 12.17552
> Ce 13.52835 9.46985 6.76418
> Ce 13.52835 9.46985 1.35284
> Ce 13.52835 4.05851 12.17552
> Ce 13.52835 4.05851 6.76418
> Ce 13.52835 4.05851 1.35284
> #O 1.35284 13.52836 13.52836
> O 1.35284 13.52836 8.11702
> O 1.35284 13.52836 2.70567
> O 1.35284 8.11702 13.52836
> O 1.35284 8.11702 8.11702
> O 1.35284 8.11702 2.70567
> O 1.35284 2.70567 13.52836
> O 1.35284 2.70567 8.11702
> O 1.35284 2.70567 2.70567
> O 6.76417 13.52836 13.52836
> O 6.76417 13.52836 8.11702
> O 6.76417 13.52836 2.70567
> O 6.76417 8.11702 13.52836
> O 6.76417 8.11702 8.11702
> O 6.76417 8.11702 2.70567
> O 6.76417 2.70567 13.52836
> O 6.76417 2.70567 8.11702
> O 6.76417 2.70567 2.70567
> O 12.17552 13.52836 13.52836
> O 12.17552 13.52836 8.11702
> O 12.17552 13.52836 2.70567
> O 12.17552 8.11702 13.52836
> O 12.17552 8.11702 8.11702
> O 12.17552 8.11702 2.70567
> O 12.17552 2.70567 13.52836
> O 12.17552 2.70567 8.11702
> O 12.17552 2.70567 2.70567
> O 1.35284 10.82268 10.82268
> O 1.35284 10.82268 5.41135
> O 1.35284 10.82268 0.00000
> O 1.35284 5.41135 10.82268
> O 1.35284 5.41135 5.41135
> O 1.35284 5.41135 0.00000
> O 1.35284 0.00000 10.82268
> O 1.35284 0.00000 5.41135
> O 1.35284 0.00000 0.00000
> O 6.76417 10.82268 10.82268
> O 6.76417 10.82268 5.41135
> O 6.76417 10.82268 0.00000
> O 6.76417 5.41135 10.82268
> O 6.76417 5.41135 5.41135
> O 6.76417 5.41135 0.00000
> O 6.76417 0.00000 10.82268
> O 6.76417 0.00000 5.41135
> O 6.76417 0.00000 0.00000
> O 12.17552 10.82268 10.82268
> O 12.17552 10.82268 5.41135
> O 12.17552 10.82268 0.00000
> O 12.17552 5.41135 10.82268
> O 12.17552 5.41135 5.41135
> O 12.17552 5.41135 0.00000
> O 12.17552 0.00000 10.82268
> O 12.17552 0.00000 5.41135
> O 12.17552 0.00000 0.00000
> O 4.05851 10.82268 13.52836
> O 4.05851 10.82268 8.11702
> O 4.05851 10.82268 2.70567
> O 4.05851 5.41135 13.52836
> O 4.05851 5.41135 8.11702
> O 4.05851 5.41135 2.70567
> O 4.05851 0.00000 13.52836
> O 4.05851 0.00000 8.11702
> O 4.05851 0.00000 2.70567
> O 9.46984 10.82268 13.52836
> O 9.46984 10.82268 8.11702
> O 9.46984 10.82268 2.70567
> O 9.46984 5.41135 13.52836
> O 9.46984 5.41135 8.11702
> O 9.46984 5.41135 2.70567
> O 9.46984 0.00000 13.52836
> O 9.46984 0.00000 8.11702
> O 9.46984 0.00000 2.70567
> O 14.88119 10.82268 13.52836
> O 14.88119 10.82268 8.11702
> O 14.88119 10.82268 2.70567
> O 14.88119 5.41135 13.52836
> O 14.88119 5.41135 8.11702
> O 14.88119 5.41135 2.70567
> O 14.88119 0.00000 13.52836
> O 14.88119 0.00000 8.11702
> O 14.88119 0.00000 2.70567
> O 4.05851 13.52836 10.82268
> O 4.05851 13.52836 5.41135
> O 4.05851 13.52836 0.00000
> O 4.05851 8.11702 10.82268
> O 4.05851 8.11702 5.41135
> O 4.05851 8.11702 0.00000
> O 4.05851 2.70567 10.82268
> O 4.05851 2.70567 5.41135
> O 4.05851 2.70567 0.00000
> O 9.46984 13.52836 10.82268
> O 9.46984 13.52836 5.41135
> O 9.46984 13.52836 0.00000
> O 9.46984 8.11702 10.82268
> O 9.46984 8.11702 5.41135
> O 9.46984 8.11702 0.00000
> O 9.46984 2.70567 10.82268
> O 9.46984 2.70567 5.41135
> O 9.46984 2.70567 0.00000
> O 14.88119 13.52836 10.82268
> O 14.88119 13.52836 5.41135
> O 14.88119 13.52836 0.00000
> O 14.88119 8.11702 10.82268
> O 14.88119 8.11702 5.41135
> O 14.88119 8.11702 0.00000
> O 14.88119 2.70567 10.82268
> O 14.88119 2.70567 5.41135
> O 14.88119 2.70567 0.00000
> O 1.35284 13.52836 10.82268
> O 1.35284 13.52836 5.41135
> O 1.35284 13.52836 0.00000
> O 1.35284 8.11702 10.82268
> O 1.35284 8.11702 5.41135
> O 1.35284 8.11702 0.00000
> O 1.35284 2.70567 10.82268
> O 1.35284 2.70567 5.41135
> O 1.35284 2.70567 0.00000
> O 6.76417 13.52836 10.82268
> O 6.76417 13.52836 5.41135
> O 6.76417 13.52836 0.00000
> O 6.76417 8.11702 10.82268
> O 6.76417 8.11702 5.41135
> O 6.76417 8.11702 0.00000
> O 6.76417 2.70567 10.82268
> O 6.76417 2.70567 5.41135
> O 6.76417 2.70567 0.00000
> O 12.17552 13.52836 10.82268
> O 12.17552 13.52836 5.41135
> O 12.17552 13.52836 0.00000
> O 12.17552 8.11702 10.82268
> O 12.17552 8.11702 5.41135
> O 12.17552 8.11702 0.00000
> O 12.17552 2.70567 10.82268
> O 12.17552 2.70567 5.41135
> O 12.17552 2.70567 0.00000
> O 1.35284 10.82268 13.52836
> O 1.35284 10.82268 8.11702
> O 1.35284 10.82268 2.70567
> O 1.35284 5.41135 13.52836
> O 1.35284 5.41135 8.11702
> O 1.35284 5.41135 2.70567
> O 1.35284 0.00000 13.52836
> O 1.35284 0.00000 8.11702
> O 1.35284 0.00000 2.70567
> O 6.76417 10.82268 13.52836
> O 6.76417 10.82268 8.11702
> O 6.76417 10.82268 2.70567
> O 6.76417 5.41135 13.52836
> O 6.76417 5.41135 8.11702
> O 6.76417 5.41135 2.70567
> O 6.76417 0.00000 13.52836
> O 6.76417 0.00000 8.11702
> O 6.76417 0.00000 2.70567
> O 12.17552 10.82268 13.52836
> O 12.17552 10.82268 8.11702
> O 12.17552 10.82268 2.70567
> O 12.17552 5.41135 13.52836
> O 12.17552 5.41135 8.11702
> O 12.17552 5.41135 2.70567
> O 12.17552 0.00000 13.52836
> O 12.17552 0.00000 8.11702
> O 12.17552 0.00000 2.70567
> O 4.05851 10.82268 10.82268
> O 4.05851 10.82268 5.41135
> O 4.05851 10.82268 0.00000
> O 4.05851 5.41135 10.82268
> O 4.05851 5.41135 5.41135
> O 4.05851 5.41135 0.00000
> O 4.05851 0.00000 10.82268
> O 4.05851 0.00000 5.41135
> O 4.05851 0.00000 0.00000
> O 9.46984 10.82268 10.82268
> O 9.46984 10.82268 5.41135
> O 9.46984 10.82268 0.00000
> O 9.46984 5.41135 10.82268
> O 9.46984 5.41135 5.41135
> O 9.46984 5.41135 0.00000
> O 9.46984 0.00000 10.82268
> O 9.46984 0.00000 5.41135
> O 9.46984 0.00000 0.00000
> O 14.88119 10.82268 10.82268
> O 14.88119 10.82268 5.41135
> O 14.88119 10.82268 0.00000
> O 14.88119 5.41135 10.82268
> O 14.88119 5.41135 5.41135
> O 14.88119 5.41135 0.00000
> O 14.88119 0.00000 10.82268
> O 14.88119 0.00000 5.41135
> O 14.88119 0.00000 0.00000
> O 4.05851 13.52836 13.52836
> O 4.05851 13.52836 8.11702
> O 4.05851 13.52836 2.70567
> O 4.05851 8.11702 13.52836
> O 4.05851 8.11702 8.11702
> O 4.05851 8.11702 2.70567
> O 4.05851 2.70567 13.52836
> O 4.05851 2.70567 8.11702
> O 4.05851 2.70567 2.70567
> O 9.46984 13.52836 13.52836
> O 9.46984 13.52836 8.11702
> O 9.46984 13.52836 2.70567
> O 9.46984 8.11702 13.52836
> O 9.46984 8.11702 8.11702
> O 9.46984 8.11702 2.70567
> O 9.46984 2.70567 13.52836
> O 9.46984 2.70567 8.11702
> O 9.46984 2.70567 2.70567
> O 14.88119 13.52836 13.52836
> O 14.88119 13.52836 8.11702
> O 14.88119 13.52836 2.70567
> O 14.88119 8.11702 13.52836
> O 14.88119 8.11702 8.11702
> O 14.88119 8.11702 2.70567
> O 14.88119 2.70567 13.52836
> O 14.88119 2.70567 8.11702
> O 14.88119 2.70567 2.70567
> &END COORD
> &KIND Ce
> BASIS_SET DZVP-GTH-PADE
> POTENTIAL GTH-PADE-q12
> &DFT_PLUS_U
> L 3
> U_MINUS_J [eV] 5
> &END DFT_PLUS_U
> &END KIND
> &KIND O
> BASIS_SET DZVP-GTH-PADE
> POTENTIAL GTH-PADE-q6
> &END KIND
> &END SUBSYS
> &END FORCE_EVAL
>
> The output cell_d-pos-1.xyz is the same as the initial starting
> coordinates
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