[CPMD-list] Au clusters with Vanderbilt USPP
Yvan Girard
yvan at ms.ifoc.kyushu-u.ac.jp
Sat Nov 27 05:47:40 CET 2004
Dear CPMD users,
For my very first steps with the CPMD calculations, I would like to perform
some geometry optimization of Au clusters. I tried several pseudopotentials
and functionnals, but I am a bit surprised by the results with VDB pp. Even
with the simple Au-Au dimer, and after a very long geometry optimization, I
finally get an interatomic distance of 3.4 angstroms (about 2.6 A expected).
With Trouiller-Martin pseudopotentials, I get a reasonable distance (2.5 A)
even with a very low cutoff value (40 Ry).
Can you tell me what I did wrong?
Yvan.
********************************************
INPUT FILE - starting geometry ~ 3 Ang.
with pp from http://www.physics.rutgers.edu/~dhv/uspp/uspp-cur/Work/079-Au/
***********************
&CPMD
OPTIMIZE GEOMETRY XYZ SAMPLE
1
CONVERGENCE ORBITALS
1E-6
CONVERGENCE GEOMETRY
1E-4
MEMORY BIG
PCG
RHOOUT
STORE
35
&END
&DFT
FUNCTIONAL GGA
GC-CUTOFF
5.0E-06
&END
&SYSTEM
SYMMETRY
0
ANGSTROM
CELL
8 1 1 0.0 0.0 0.0
CUTOFF
40.
&END
&ATOMS
*079-Au-gpw-n-campos.uspp NEWF BINARY TPSEU
LMAX=D
2
4.359520854514 5.319510212275 5.000738935348
3.413895342766 2.595692582913 5.169297862747
&END
***************************************
Parts of the OUTPUT file :
**********************************
PROGRAM CPMD STARTED AT: Thu Nov 18 23:55:47 2004
VERSION 3.9.1
THE JOB WAS SUBMITTED BY: yvan
OPTIMIZATION OF IONIC POSITIONS
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 10000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 35 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR
STORE ELECTRON DENSITY AT THE END OF THE RUN
FICTITIOUS ELECTRON MASS: 400.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED CG
THRESHOLD FOR THE HESSIAN IS 0.5000
FULL ELECTRONIC GRADIENT IS USED
CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 1.000000E-04
GEOMETRY OPTIMIZATION BY GDIIS/BFGS
SIZE OF GDIIS MATRIX: 5
GEOMETRY OPTIMIZATION IS SAVED ON FILE GEO_OPT.xyz
EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION)
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000
EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: NONE
LDA XC THROUGH PADE APPROXIMATION
S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996)
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 5.00000E-06
EXCHANGE ENERGY
[GGA: J.P. PERDEW ET AL. PHYS. REV. B 46, 6671 (1992)]
CORRELATION ENERGY
[GGA: J.P. PERDEW ET AL. PHYS. REV. B 46, 6671
(1992)]
*** DETSP| THE NEW SIZE OF THE PROGRAM IS 1324/ 18900 kBYTES ***
>>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<<
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 Au 8.452391 10.132538 7.399639 3
2 Au 6.665417 4.985269 7.718169 3
****************************************************************
NUMBER OF STATES: 11
NUMBER OF ELECTRONS: 22.00000
CHARGE: 0.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
============================================================
| pseudopotential report: version 7.3.5 date 11- 9-2004 |
------------------------------------------------------------
| Au (US s-loc) Perdew Wang 1991 exchange-corr |
| z = 79.00 zv = 11.00 exfact = 4.00000 |
| etot =-101.80699 |
| index orbital occupation energy |
| 1 520 9.50 -0.67 |
| 2 600 1.00 -0.52 |
| 3 610 0.50 -0.11 |
| keyps = 3 ifpcor = 1 |
| rinner = 1.10 for L= 1 |
| rinner = 1.10 for L= 2 |
| rinner = 1.10 for L= 3 |
| rinner = 1.10 for L= 4 |
| rinner = 1.10 for L= 5 |
| new generation scheme: |
| nbeta = 3 kkbeta = 747 rcloc = 2.3723 |
| ibeta l epsilon rcut iptype |
| 1 1 -0.11 2.37 3 |
| 2 2 -0.67 1.90 2 |
| 3 2 0.00 1.90 2 |
| npf = 8 ptryc = 10.000 |
| lloc = 0 eloc = -0.523 |
| ifqopt = 3 nqf = 8 qtryc = 10.000 |
| all electron calculation used koelling-harmon equation |
| ************logarithmic mesh************ |
============================================================
****************************************************************
* ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL *
* Au 196.9670 1.2000 YES VANDERBILT *
****************************************************************
OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
NUMBER OF CPUS PER TASK 1
OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
*** RGGEN| THE NEW SIZE OF THE PROGRAM IS 6244/ 31408 kBYTES ***
************************** SUPERCELL ***************************
THIS IS AN ISOLATED SYSTEM CALCULATION
POISSON EQUATION SOLVER : HOCKNEY
COULOMB SMOOTHING RADIUS : 1.080
SYMMETRY: SIMPLE CUBIC
LATTICE CONSTANT(a.u.): 15.11781
CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 3455.14651
LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661
REAL SPACE MESH: 64 64 64
WAVEFUNCTION CUTOFF(RYDBERG): 40.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 160.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 7386
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 59133
****************************************************************
*** RINFORCE| THE NEW SIZE OF THE PROGRAM IS 21540/ 47868 kBYTES ***
*** FFTPRP| THE NEW SIZE OF THE PROGRAM IS 28956/ 45612 kBYTES ***
*** CLUSTER| THE NEW SIZE OF THE PROGRAM IS 31720/ 48224 kBYTES ***
GENERATE ATOMIC BASIS SET
Au SLATER ORBITALS
5D ALPHA= 3.9625 OCCUPATION=10.00
6S ALPHA= 0.8810 OCCUPATION= 1.00
INITIALIZATION TIME: 14.71 SECONDS
*** GMOPTS| THE NEW SIZE OF THE PROGRAM IS 32120/ 54340 kBYTES ***
*** PHFAC| THE NEW SIZE OF THE PROGRAM IS 32312/ 80952 kBYTES ***
*** ATOMWF| THE NEW SIZE OF THE PROGRAM IS 34408/ 83036 kBYTES ***
ATRHO| CHARGE(R-SPACE): 22.000000 (G-SPACE): 22.000000
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Au 8.452391 10.132538 7.399639
2 Au 6.665417 4.985269 7.718169
****************************************************************
DEGREES OF FREEDOM FOR SYSTEM: 3
INITIALIZE EMPIRICAL HESSIAN
<<<<< ASSUMED BONDS >>>>>
2 <--> 1
TOTAL NUMBER OF MOLECULAR STRUCTURES: 1
****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 Au 8.452391 10.132538 7.399639
2 Au 6.665417 4.985269 7.718169
****************************************************************
CPU TIME FOR INITIALIZATION 3.15 SECONDS
================================================================
= GEOMETRY OPTIMIZATION =
================================================================
NFI GEMAX CNORM ETOT DETOT TCPU
EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
[...]
[...]
[...]
[...]
[...]
****************************************************************
*** TOTAL STEP NR. 9967 GEOMETRY STEP NR. 148 ***
*** GNMAX= 2.082271E-02 [1.77E-03] ETOT= -71.375704 ***
*** GNORM= 1.378784E-02 DETOT= 1.486E-05 ***
*** CNSTR= 0.000000E+00 TCPU= 141.87 ***
****************************************************************
1 2.737E-04 3.911E-05 -71.375701 2.312E-06 2.09
2 2.409E-04 3.401E-05 -71.375704 -2.259E-06 2.08
3 1.980E-04 2.747E-05 -71.375706 -2.360E-06 2.08
4 1.591E-04 2.173E-05 -71.375707 -1.573E-06 2.07
5 1.273E-04 1.721E-05 -71.375708 -9.093E-07 2.07
6 1.019E-04 1.374E-05 -71.375709 -4.998E-07 2.07
7 8.167E-05 1.106E-05 -71.375709 -2.648E-07 2.08
8 6.550E-05 8.995E-06 -71.375709 -1.324E-07 2.08
RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
9 5.256E-05 7.387E-06 -71.375709 -5.869E-08 2.07
10 4.220E-05 6.125E-06 -71.375709 -1.853E-08 2.07
11 3.389E-05 5.126E-06 -71.375709 2.500E-09 2.09
12 2.577E-05 4.140E-06 -71.375709 1.833E-08 2.08
13 1.961E-05 3.323E-06 -71.375709 2.760E-08 2.08
14 1.575E-05 2.681E-06 -71.375709 2.928E-08 2.07
15 1.329E-05 2.176E-06 -71.375709 2.694E-08 2.09
16 1.183E-05 1.765E-06 -71.375709 2.317E-08 2.08
17 1.063E-05 1.422E-06 -71.375709 1.904E-08 2.08
18 9.609E-06 1.130E-06 -71.375709 1.494E-08 2.07
19 8.742E-06 8.838E-07 -71.375709 1.099E-08 2.07
20 7.996E-06 6.816E-07 -71.375709 7.339E-09 2.08
21 7.346E-06 5.265E-07 -71.375709 4.173E-09 2.09
22 6.750E-06 4.191E-07 -71.375709 1.815E-09 2.09
23 6.199E-06 3.628E-07 -71.375709 4.852E-11 2.09
24 5.681E-06 3.452E-07 -71.375709 -1.123E-09 2.09
25 5.187E-06 3.449E-07 -71.375709 -1.801E-09 2.08
26 4.711E-06 3.446E-07 -71.375709 -2.116E-09 2.09
27 4.252E-06 3.355E-07 -71.375709 -2.188E-09 2.07
28 3.813E-06 3.150E-07 -71.375709 -2.118E-09 2.07
29 3.400E-06 2.840E-07 -71.375709 -1.981E-09 2.07
30 3.021E-06 2.457E-07 -71.375709 -1.836E-09 2.08
31 2.681E-06 2.046E-07 -71.375709 -1.718E-09 2.09
32 2.383E-06 1.656E-07 -71.375709 -1.644E-09 2.50
33 2.128E-06 1.333E-07 -71.375709 -1.615E-09 2.49
================================================================
= END OF GEOMETRY OPTIMIZATION =
================================================================
RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
DENSITY WRITTEN TO FILE ./DENSITY
****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************
ATOM COORDINATES GRADIENTS (-FORCES)
1 Au 8.6119 10.5919 7.3712 -2.086E-02 1.128E-02 3.680E-03
2 Au 6.5060 4.5259 7.7466 2.047E-02 -1.151E-02 -3.616E-03
****************************************************************
ELECTRONIC GRADIENT:
MAX. COMPONENT = 2.12752E-06 NORM = 1.33338E-07
NUCLEAR GRADIENT:
MAX. COMPONENT = 2.08582E-02 NORM = 1.37869E-02
TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 22.000000
IN R-SPACE = 22.000000
VANDERBILT AUGMENTATION CHARGES (MEAN VALUE PER ATOM)
ATOM TYPE NR. OF ATOMS CHARGE
Au 2 2.989
(K+E1+L+N+X) TOTAL ENERGY = -71.37570921 A.U.
(K) KINETIC ENERGY = 9.96017820 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -75.01998936 A.U.
(S) ESELF = 80.45335988 A.U.
(R) ESR = 0.00000157 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = 31.60118695 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = -24.03266576 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -13.88441923 A.U.
GRADIENT CORRECTION ENERGY = 0.01582107 A.U.
****************************************************************
================================================================
BIG MEMORY ALLOCATIONS
SCR 1766222 SCR 1766216
YLMB 1478325 SCR 1114753
PSI 1098500 QRL 903600
XF 549250 YF 549250
RHOE 274625 HGPOT 274625
----------------------------------------------------------------
[PEAK NUMBER 107] PEAK MEMORY 8568493 = 68.5 MBytes
================================================================
****************************************************************
* *
* TIMING *
* *
****************************************************************
SUBROUTINE CALLS CPU TIME ELAPSED TIME
RHOV 10001 2696.18 2735.50
HIP 10001 2688.94 2730.54
NEWD 10001 2572.46 2606.66
GCENER 10150 2411.98 2446.98
FWFFT 70753 1955.35 1983.73
INVFFT 70604 1770.11 1796.58
S_INVFFT 120012 1611.24 1631.97
FFT-G/S 360036 1181.21 1198.60
S_FWFFT 60006 937.43 952.64
VPSI 10002 625.46 637.39
RHOOFR 10001 585.01 597.16
RNLSM1 20152 424.59 698.71
XCENER 10150 386.14 392.24
PHASE 141357 379.77 385.84
GRADEN 10150 368.01 373.76
NLFORCE 10000 294.59 298.43
VOFRHOH 10001 239.94 243.15
VOFRHOB 10001 212.65 215.08
RNLSM2 2353 154.26 248.11
COREC 10150 143.63 145.63
OVLAP 20149 72.21 103.80
EICALC 10001 62.36 63.50
PCGRAD 10000 45.82 46.28
FORCES 10000 38.81 39.82
ROTATE 10000 31.70 32.48
RGSVAN 10148 31.07 31.46
----------------------------------------------------------------
TOTAL TIME 21920.92 22636.03
****************************************************************
CPU TIME : 6 HOURS 5 MINUTES 44.65 SECONDS
ELAPSED TIME : 6 HOURS 17 MINUTES 43.15 SECONDS
PROGRAM CPMD ENDED AT: Fri Nov 19 06:13:31 2004
________________
Yvan Girard
Institute for Materials Chemistry and Engineering
Kyushu University
Fukuoka 812-8581, Japan
http://trout.scc.kyushu-u.ac.jp/yoshizawaJ/Yoshizawa-lab-Eng/index-eng.htm
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