Atoms are not relaxing, but successful optimization
Samuel Lamphier
samuell... at gmail.com
Thu Mar 22 13:17:07 UTC 2012
Thank you for your response, I used crystal maker to derive a 2x2x2
supercell, I exported the orthogonal coordinates directly. However, I
thought that if I incorporated a vacancy that I would see a much
larger relaxation as I do using classical simulations. The change was
on the order of 0.000001 for cp2k and during classical simulations, I
observed changes of 0.1 to 1.5A during relaxation.
On Mar 21, 2:45 pm, Nathaniel Swenson <nate... at gmail.com> 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
>
> ...
>
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