<div>Is you system perfect fluorite structure obtained from converting a crystal structure in fractional coords?<br></div><div><br></div><div>If so it basically can't/won't move due to symmetry. </div><div><br></div><div>Matt</div><div><br></div>On Wednesday, March 21, 2012 6:45:47 PM UTC, Nathaniel Swenson wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">Hello,
<br>
<br>My greatest apologies if you have already checked this, but this is a
<br>simple point of clarification:
<br>
<br>The cell_d-pos-1.xyz file typically should contain not just ONE set of
<br>coordinates, but it should have sets of coordinates from ALL the
<br>geometry optimization steps, all in one file. Typically, the first
<br>set of coordinates that appear in this file are your input
<br>coordinates, so if you are simply opening this file with a
<br>visualization program, this could explain why you are only getting
<br>your input coordinates back. On the contrary, the last set of
<br>coordinates in the file should be your optimized coordinates.
<br>
<br>How many sets of coordinates are showing up in your cell_d-pos-1.xyz
<br>file?
<br>
<br>Best wishes,
<br>Nathaniel Swenson
<br>Northwestern University
<br>
<br>
<br>On Mar 21, 12:12 pm, Samuel Lamphier <<a>samuell...@gmail.com</a>> wrote:
<br>> Hello all, I am modeling cerium oxide nano particles. I have prepared
<br>> input file with high cutoffs, however, I have had good luck with
<br>> optimizations. Then I discovered a problem, my atoms are not relaxing,
<br>> is there something I am doing incorrectly?
<br>>
<br>> &GLOBAL
<br>> PRINT_LEVEL LOW
<br>> PROJECT_NAME cell_d
<br>> RUN_TYPE CELL_OPT
<br>> FLUSH_SHOULD_FLUSH T
<br>> &END GLOBAL
<br>> &MOTION
<br>> &GEO_OPT
<br>> TYPE MINIMIZATION
<br>> OPTIMIZER BFGS
<br>> MAX_ITER 5000
<br>> MAX_DR 2.9999999999999997E-05
<br>> MAX_FORCE 5.0000000000000003E-06
<br>> RMS_DR 1.4999999999999999E-05
<br>> RMS_FORCE 5.0000000000000001E-06
<br>> STEP_START_VAL 1
<br>> &PRINT
<br>> &PROGRAM_RUN_INFO
<br>> &END PROGRAM_RUN_INFO
<br>> &END PRINT
<br>> &END GEO_OPT
<br>> &CELL_OPT
<br>> OPTIMIZER CG
<br>> MAX_ITER 3000
<br>> MAX_DR 3.0000000000000001E-05
<br>> MAX_FORCE 5.0000000000000000E-06
<br>> RMS_DR 1.5000000000000000E-05
<br>> RMS_FORCE 2.9999999999999997E-06
<br>> STEP_START_VAL 1
<br>> TYPE GEO_OPT
<br>> PRESSURE_TOLERANCE 1.0000000000000000E-01
<br>> &CG
<br>> MAX_STEEP_STEPS 0
<br>> RESTART_LIMIT 9.4999999999999996E-01
<br>> &LINE_SEARCH
<br>> TYPE 2PNT
<br>> &END LINE_SEARCH
<br>> &END CG
<br>> &END CELL_OPT
<br>> &END MOTION
<br>> &FORCE_EVAL
<br>> METHOD QS
<br>> STRESS_TENSOR ANALYTICAL
<br>> &DFT
<br>> CHARGE 0
<br>> PLUS_U_METHOD MULLIKEN
<br>> &SCF
<br>> MAX_SCF 1000
<br>> EPS_SCF 9.9999999999999995E-08
<br>> SCF_GUESS ATOMIC
<br>> &OT T
<br>> MINIMIZER DIIS
<br>> PRECONDITIONER FULL_ALL
<br>> ENERGY_GAP 1.0000000000000000E-03
<br>> &END OT
<br>> &OUTER_SCF T
<br>> EPS_SCF 9.9999999999999995E-08
<br>> &END OUTER_SCF
<br>> &END SCF
<br>> &QS
<br>> EPS_DEFAULT 9.9999999999999998E-13
<br>> &END QS
<br>> &MGRID
<br>> CUTOFF 3.0000000000000000E+02
<br>> &END MGRID
<br>> &XC
<br>> DENSITY_CUTOFF 1.0000000000000000E-10
<br>> GRADIENT_CUTOFF 1.0000000000000000E-10
<br>> TAU_CUTOFF 1.0000000000000000E-10
<br>> &XC_GRID
<br>> XC_SMOOTH_RHO NONE
<br>> XC_DERIV SPLINE2_SMOOTH
<br>> &END XC_GRID
<br>> &XC_FUNCTIONAL NO_SHORTCUT
<br>> &PADE T
<br>> &END PADE
<br>> &END XC_FUNCTIONAL
<br>> &END XC
<br>> &PRINT
<br>> &MO_CUBES SILENT
<br>> STRIDE 1 1 1
<br>> NLUMO 0
<br>> NHOMO 1
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END MO_CUBES
<br>> &E_DENSITY_CUBE SILENT
<br>> STRIDE 1 1 1
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END E_DENSITY_CUBE
<br>> &TOT_DENSITY_CUBE SILENT
<br>> STRIDE 1 1 1
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END TOT_DENSITY_CUBE
<br>> &PDOS SILENT
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END PDOS
<br>> &MULLIKEN
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END MULLIKEN
<br>> &LOWDIN
<br>> &EACH
<br>> GEO_OPT 1
<br>> &END EACH
<br>> &END LOWDIN
<br>> &DFT_CONTROL_PARAMETERS
<br>> &END DFT_CONTROL_PARAMETERS
<br>> &PLUS_U
<br>> &END PLUS_U
<br>> &END PRINT
<br>> &END DFT
<br>> &SUBSYS
<br>> &CELL
<br>> A 16.23402000 0.000000000 0.0000000000
<br>> B 0.000000000 16.23402000 0.0000000000
<br>> C 0.000000000 0.000000000 16.234020000
<br>> PERIODIC XYZ
<br>> &END CELL
<br>> &COORD
<br>> Ce 0.00000 14.88119 14.88119
<br>> Ce 0.00000 14.88119 9.46985
<br>> Ce 0.00000 14.88119 4.05851
<br>> Ce 0.00000 9.46985 14.88119
<br>> Ce 0.00000 9.46985 9.46985
<br>> Ce 0.00000 9.46985 4.05851
<br>> Ce 0.00000 4.05851 14.88119
<br>> Ce 0.00000 4.05851 9.46985
<br>> Ce 0.00000 4.05851 4.05851
<br>> Ce 5.41134 14.88119 14.88119
<br>> Ce 5.41134 14.88119 9.46985
<br>> Ce 5.41134 14.88119 4.05851
<br>> Ce 5.41134 9.46985 14.88119
<br>> Ce 5.41134 9.46985 9.46985
<br>> Ce 5.41134 9.46985 4.05851
<br>> Ce 5.41134 4.05851 14.88119
<br>> Ce 5.41134 4.05851 9.46985
<br>> Ce 5.41134 4.05851 4.05851
<br>> Ce 10.82268 14.88119 14.88119
<br>> Ce 10.82268 14.88119 9.46985
<br>> Ce 10.82268 14.88119 4.05851
<br>> Ce 10.82268 9.46985 14.88119
<br>> Ce 10.82268 9.46985 9.46985
<br>> Ce 10.82268 9.46985 4.05851
<br>> Ce 10.82268 4.05851 14.88119
<br>> Ce 10.82268 4.05851 9.46985
<br>> Ce 10.82268 4.05851 4.05851
<br>> Ce 0.00000 12.17552 12.17552
<br>> Ce 0.00000 12.17552 6.76418
<br>> Ce 0.00000 12.17552 1.35284
<br>> Ce 0.00000 6.76418 12.17552
<br>> Ce 0.00000 6.76418 6.76418
<br>> Ce 0.00000 6.76418 1.35284
<br>> Ce 0.00000 1.35284 12.17552
<br>> Ce 0.00000 1.35284 6.76418
<br>> Ce 0.00000 1.35284 1.35284
<br>> Ce 5.41134 12.17552 12.17552
<br>> Ce 5.41134 12.17552 6.76418
<br>> Ce 5.41134 12.17552 1.35284
<br>> Ce 5.41134 6.76418 12.17552
<br>> Ce 5.41134 6.76418 6.76418
<br>> Ce 5.41134 6.76418 1.35284
<br>> Ce 5.41134 1.35284 12.17552
<br>> Ce 5.41134 1.35284 6.76418
<br>> Ce 5.41134 1.35284 1.35284
<br>> Ce 10.82268 12.17552 12.17552
<br>> Ce 10.82268 12.17552 6.76418
<br>> Ce 10.82268 12.17552 1.35284
<br>> Ce 10.82268 6.76418 12.17552
<br>> Ce 10.82268 6.76418 6.76418
<br>> Ce 10.82268 6.76418 1.35284
<br>> Ce 10.82268 1.35284 12.17552
<br>> Ce 10.82268 1.35284 6.76418
<br>> Ce 10.82268 1.35284 1.35284
<br>> Ce 2.70567 12.17552 14.88119
<br>> Ce 2.70567 12.17552 9.46985
<br>> Ce 2.70567 12.17552 4.05851
<br>> Ce 2.70567 6.76418 14.88119
<br>> Ce 2.70567 6.76418 9.46985
<br>> Ce 2.70567 6.76418 4.05851
<br>> Ce 2.70567 1.35284 14.88119
<br>> Ce 2.70567 1.35284 9.46985
<br>> Ce 2.70567 1.35284 4.05851
<br>> Ce 8.11701 12.17552 14.88119
<br>> Ce 8.11701 12.17552 9.46985
<br>> Ce 8.11701 12.17552 4.05851
<br>> Ce 8.11701 6.76418 14.88119
<br>> Ce 8.11701 6.76418 9.46985
<br>> Ce 8.11701 6.76418 4.05851
<br>> Ce 8.11701 1.35284 14.88119
<br>> Ce 8.11701 1.35284 9.46985
<br>> Ce 8.11701 1.35284 4.05851
<br>> Ce 13.52835 12.17552 14.88119
<br>> Ce 13.52835 12.17552 9.46985
<br>> Ce 13.52835 12.17552 4.05851
<br>> Ce 13.52835 6.76418 14.88119
<br>> Ce 13.52835 6.76418 9.46985
<br>> Ce 13.52835 6.76418 4.05851
<br>> Ce 13.52835 1.35284 14.88119
<br>> Ce 13.52835 1.35284 9.46985
<br>> Ce 13.52835 1.35284 4.05851
<br>> Ce 2.70567 14.88119 12.17552
<br>> Ce 2.70567 14.88119 6.76418
<br>> Ce 2.70567 14.88119 1.35284
<br>> Ce 2.70567 9.46985 12.17552
<br>> Ce 2.70567 9.46985 6.76418
<br>> Ce 2.70567 9.46985 1.35284
<br>> Ce 2.70567 4.05851 12.17552
<br>> Ce 2.70567 4.05851 6.76418
<br>> Ce 2.70567 4.05851 1.35284
<br>> Ce 8.11701 14.88119 12.17552
<br>> Ce 8.11701 14.88119 6.76418
<br>> Ce 8.11701 14.88119 1.35284
<br>> Ce 8.11701 9.46985 12.17552
<br>> Ce 8.11701 9.46985 6.76418
<br>> Ce 8.11701 9.46985 1.35284
<br>> Ce 8.11701 4.05851 12.17552
<br>> Ce 8.11701 4.05851 6.76418
<br>> Ce 8.11701 4.05851 1.35284
<br>> Ce 13.52835 14.88119 12.17552
<br>> Ce 13.52835 14.88119 6.76418
<br>> Ce 13.52835 14.88119 1.35284
<br>> Ce 13.52835 9.46985 12.17552
<br>> Ce 13.52835 9.46985 6.76418
<br>> Ce 13.52835 9.46985 1.35284
<br>> Ce 13.52835 4.05851 12.17552
<br>> Ce 13.52835 4.05851 6.76418
<br>> Ce 13.52835 4.05851 1.35284
<br>> #O 1.35284 13.52836 13.52836
<br>> O 1.35284 13.52836 8.11702
<br>> O 1.35284 13.52836 2.70567
<br>> O 1.35284 8.11702 13.52836
<br>> O 1.35284 8.11702 8.11702
<br>> O 1.35284 8.11702 2.70567
<br>> O 1.35284 2.70567 13.52836
<br>> O 1.35284 2.70567 8.11702
<br>> O 1.35284 2.70567 2.70567
<br>> O 6.76417 13.52836 13.52836
<br>> O 6.76417 13.52836 8.11702
<br>> O 6.76417 13.52836 2.70567
<br>> O 6.76417 8.11702 13.52836
<br>> O 6.76417 8.11702 8.11702
<br>> O 6.76417 8.11702 2.70567
<br>> O 6.76417 2.70567 13.52836
<br>> O 6.76417 2.70567 8.11702
<br>> O 6.76417 2.70567 2.70567
<br>> O 12.17552 13.52836 13.52836
<br>> O 12.17552 13.52836 8.11702
<br>> O 12.17552 13.52836 2.70567
<br>> O 12.17552 8.11702 13.52836
<br>> O 12.17552 8.11702 8.11702
<br>> O 12.17552 8.11702 2.70567
<br>> O 12.17552 2.70567 13.52836
<br>> O 12.17552 2.70567 8.11702
<br>> O 12.17552 2.70567 2.70567
<br>> O 1.35284 10.82268 10.82268
<br>> O 1.35284 10.82268 5.41135
<br>> O 1.35284 10.82268 0.00000
<br>> O 1.35284 5.41135 10.82268
<br>> O 1.35284 5.41135 5.41135
<br>> O 1.35284 5.41135 0.00000
<br>> O 1.35284 0.00000 10.82268
<br>> O 1.35284 0.00000 5.41135
<br>> O 1.35284 0.00000 0.00000
<br>> O 6.76417 10.82268 10.82268
<br>> O 6.76417 10.82268 5.41135
<br>> O 6.76417 10.82268 0.00000
<br>> O 6.76417 5.41135 10.82268
<br>> O 6.76417 5.41135 5.41135
<br>> O 6.76417 5.41135 0.00000
<br>> O 6.76417 0.00000 10.82268
<br>> O 6.76417 0.00000 5.41135
<br>> O 6.76417 0.00000 0.00000
<br>> O 12.17552 10.82268 10.82268
<br>> O 12.17552 10.82268 5.41135
<br>> O 12.17552 10.82268 0.00000
<br>> O 12.17552 5.41135 10.82268
<br>> O 12.17552 5.41135 5.41135
<br>> O 12.17552 5.41135 0.00000
<br>> O 12.17552 0.00000 10.82268
<br>> O 12.17552 0.00000 5.41135
<br>> O 12.17552 0.00000 0.00000
<br>> O 4.05851 10.82268 13.52836
<br>> O 4.05851 10.82268 8.11702
<br>> O 4.05851 10.82268 2.70567
<br>> O 4.05851 5.41135 13.52836
<br>> O 4.05851 5.41135 8.11702
<br>> O 4.05851 5.41135 2.70567
<br>> O 4.05851 0.00000 13.52836
<br>> O 4.05851 0.00000 8.11702
<br>> O 4.05851 0.00000 2.70567
<br>> O 9.46984 10.82268 13.52836
<br>> O 9.46984 10.82268 8.11702
<br>> O 9.46984 10.82268 2.70567
<br>> O 9.46984 5.41135 13.52836
<br>> O 9.46984 5.41135 8.11702
<br>> O 9.46984 5.41135 2.70567
<br>> O 9.46984 0.00000 13.52836
<br>> O 9.46984 0.00000 8.11702
<br>> O 9.46984 0.00000 2.70567
<br>> O 14.88119 10.82268 13.52836
<br>> O 14.88119 10.82268 8.11702
<br>> O 14.88119 10.82268 2.70567
<br>> O 14.88119 5.41135 13.52836
<br>> O 14.88119 5.41135 8.11702
<br>> O 14.88119 5.41135 2.70567
<br>> O 14.88119 0.00000 13.52836
<br>> O 14.88119 0.00000 8.11702
<br>> O 14.88119 0.00000 2.70567
<br>> O 4.05851 13.52836 10.82268
<br>> O 4.05851 13.52836 5.41135
<br>> O 4.05851 13.52836 0.00000
<br>> O 4.05851 8.11702 10.82268
<br>> O 4.05851 8.11702 5.41135
<br>> O 4.05851 8.11702 0.00000
<br>> O 4.05851 2.70567 10.82268
<br>> O 4.05851 2.70567 5.41135
<br>> O 4.05851 2.70567 0.00000
<br>> O 9.46984 13.52836 10.82268
<br>> O 9.46984 13.52836 5.41135
<br>> O 9.46984 13.52836 0.00000
<br>> O 9.46984 8.11702 10.82268
<br>> O 9.46984 8.11702 5.41135
<br>> O 9.46984 8.11702 0.00000
<br>> O 9.46984 2.70567 10.82268
<br>> O 9.46984 2.70567 5.41135
<br>> O 9.46984 2.70567 0.00000
<br>> O 14.88119 13.52836 10.82268
<br>> O 14.88119 13.52836 5.41135
<br>> O 14.88119 13.52836 0.00000
<br>> O 14.88119 8.11702 10.82268
<br>> O 14.88119 8.11702 5.41135
<br>> O 14.88119 8.11702 0.00000
<br>> O 14.88119 2.70567 10.82268
<br>> O 14.88119 2.70567 5.41135
<br>> O 14.88119 2.70567 0.00000
<br>> O 1.35284 13.52836 10.82268
<br>> O 1.35284 13.52836 5.41135
<br>> O 1.35284 13.52836 0.00000
<br>> O 1.35284 8.11702 10.82268
<br>> O 1.35284 8.11702 5.41135
<br>> O 1.35284 8.11702 0.00000
<br>> O 1.35284 2.70567 10.82268
<br>> O 1.35284 2.70567 5.41135
<br>> O 1.35284 2.70567 0.00000
<br>> O 6.76417 13.52836 10.82268
<br>> O 6.76417 13.52836 5.41135
<br>> O 6.76417 13.52836 0.00000
<br>> O 6.76417 8.11702 10.82268
<br>> O 6.76417 8.11702 5.41135
<br>> O 6.76417 8.11702 0.00000
<br>> O 6.76417 2.70567 10.82268
<br>> O 6.76417 2.70567 5.41135
<br>> O 6.76417 2.70567 0.00000
<br>> O 12.17552 13.52836 10.82268
<br>> O 12.17552 13.52836 5.41135
<br>> O 12.17552 13.52836 0.00000
<br>> O 12.17552 8.11702 10.82268
<br>> O 12.17552 8.11702 5.41135
<br>> O 12.17552 8.11702 0.00000
<br>> O 12.17552 2.70567 10.82268
<br>> O 12.17552 2.70567 5.41135
<br>> O 12.17552 2.70567 0.00000
<br>> O 1.35284 10.82268 13.52836
<br>> O 1.35284 10.82268 8.11702
<br>> O 1.35284 10.82268 2.70567
<br>> O 1.35284 5.41135 13.52836
<br>> O 1.35284 5.41135 8.11702
<br>> O 1.35284 5.41135 2.70567
<br>> O 1.35284 0.00000 13.52836
<br>> O 1.35284 0.00000 8.11702
<br>> O 1.35284 0.00000 2.70567
<br>> O 6.76417 10.82268 13.52836
<br>> O 6.76417 10.82268 8.11702
<br>> O 6.76417 10.82268 2.70567
<br>> O 6.76417 5.41135 13.52836
<br>> O 6.76417 5.41135 8.11702
<br>> O 6.76417 5.41135 2.70567
<br>> O 6.76417 0.00000 13.52836
<br>> O 6.76417 0.00000 8.11702
<br>> O 6.76417 0.00000 2.70567
<br>> O 12.17552 10.82268 13.52836
<br>> O 12.17552 10.82268 8.11702
<br>> O 12.17552 10.82268 2.70567
<br>> O 12.17552 5.41135 13.52836
<br>> O 12.17552 5.41135 8.11702
<br>> O 12.17552 5.41135 2.70567
<br>> O 12.17552 0.00000 13.52836
<br>> O 12.17552 0.00000 8.11702
<br>> O 12.17552 0.00000 2.70567
<br>> O 4.05851 10.82268 10.82268
<br>> O 4.05851 10.82268 5.41135
<br>> O 4.05851 10.82268 0.00000
<br>> O 4.05851 5.41135 10.82268
<br>> O 4.05851 5.41135 5.41135
<br>> O 4.05851 5.41135 0.00000
<br>> O 4.05851 0.00000 10.82268
<br>> O 4.05851 0.00000 5.41135
<br>> O 4.05851 0.00000 0.00000
<br>> O 9.46984 10.82268 10.82268
<br>> O 9.46984 10.82268 5.41135
<br>> O 9.46984 10.82268 0.00000
<br>> O 9.46984 5.41135 10.82268
<br>> O 9.46984 5.41135 5.41135
<br>> O 9.46984 5.41135 0.00000
<br>> O 9.46984 0.00000 10.82268
<br>> O 9.46984 0.00000 5.41135
<br>> O 9.46984 0.00000 0.00000
<br>> O 14.88119 10.82268 10.82268
<br>> O 14.88119 10.82268 5.41135
<br>> O 14.88119 10.82268 0.00000
<br>> O 14.88119 5.41135 10.82268
<br>> O 14.88119 5.41135 5.41135
<br>> O 14.88119 5.41135 0.00000
<br>> O 14.88119 0.00000 10.82268
<br>> O 14.88119 0.00000 5.41135
<br>> O 14.88119 0.00000 0.00000
<br>> O 4.05851 13.52836 13.52836
<br>> O 4.05851 13.52836 8.11702
<br>> O 4.05851 13.52836 2.70567
<br>> O 4.05851 8.11702 13.52836
<br>> O 4.05851 8.11702 8.11702
<br>> O 4.05851 8.11702 2.70567
<br>> O 4.05851 2.70567 13.52836
<br>> O 4.05851 2.70567 8.11702
<br>> O 4.05851 2.70567 2.70567
<br>> O 9.46984 13.52836 13.52836
<br>> O 9.46984 13.52836 8.11702
<br>> O 9.46984 13.52836 2.70567
<br>> O 9.46984 8.11702 13.52836
<br>> O 9.46984 8.11702 8.11702
<br>> O 9.46984 8.11702 2.70567
<br>> O 9.46984 2.70567 13.52836
<br>> O 9.46984 2.70567 8.11702
<br>> O 9.46984 2.70567 2.70567
<br>> O 14.88119 13.52836 13.52836
<br>> O 14.88119 13.52836 8.11702
<br>> O 14.88119 13.52836 2.70567
<br>> O 14.88119 8.11702 13.52836
<br>> O 14.88119 8.11702 8.11702
<br>> O 14.88119 8.11702 2.70567
<br>> O 14.88119 2.70567 13.52836
<br>> O 14.88119 2.70567 8.11702
<br>> O 14.88119 2.70567 2.70567
<br>> &END COORD
<br>> &KIND Ce
<br>> BASIS_SET DZVP-GTH-PADE
<br>> POTENTIAL GTH-PADE-q12
<br>> &DFT_PLUS_U
<br>> L 3
<br>> U_MINUS_J [eV] 5
<br>> &END DFT_PLUS_U
<br>> &END KIND
<br>> &KIND O
<br>> BASIS_SET DZVP-GTH-PADE
<br>> POTENTIAL GTH-PADE-q6
<br>> &END KIND
<br>> &END SUBSYS
<br>> &END FORCE_EVAL
<br>>
<br>> The output cell_d-pos-1.xyz is the same as the initial starting
<br>> coordinates</blockquote>