Atoms are not relaxing, but successful optimization
Matt W
MattWa... at gmail.com
Wed Mar 21 20:13:00 UTC 2012
Is you system perfect fluorite structure obtained from converting a crystal
structure in fractional coords?
If so it basically can't/won't move due to symmetry.
Matt
On Wednesday, March 21, 2012 6:45:47 PM UTC, Nathaniel Swenson wrote:
>
> 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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