Localization
Nuri Yazdani
nuri.a.... at gmail.com
Mon Dec 1 13:50:03 UTC 2014
Hello everyone,
I am trying to print out the Wannier centers and Total Dipoles for my
system during MD, which I have never done before. Following the
thread: https://groups.google.com/forum/#!searchin/cp2k/total$20dipole/cp2k/o6ZIVNNP-gc/XSjFwBBZAHwJ
, I made my input file as attached. When I include the Localization command
I get an error in the input file parsing. Then, as suggested in the
mentioned thread, I removed the Localization command, as shown in my .inp
file. The problem now is that the localization doesnt seem to get performed
at all! I have also attached my output file. Any help would be highly
appreciated!
Cheers,
Nuri
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DBCSR| Multiplication driver SMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Multiplication size stacks 3
DBCSR| Use subcommunicators T
DBCSR| Use MPI combined types F
DBCSR| Use MPI memory allocation T
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2014-12-01 14:00:26.445
***** ** *** *** ** PROGRAM STARTED ON dahu2.ee.ethz.ch
** **** ****** PROGRAM STARTED BY yazdanin
***** ** ** ** ** PROGRAM PROCESS ID 122094
**** ** ******* ** PROGRAM STARTED IN /home/IIS-lnedata/CP2K/Examples/SS/Cl
/251/01
CP2K| version string: CP2K version 2.6 (Development Version)
CP2K| source code revision number: svn:14377
CP2K| is freely available from http://www.cp2k.org/
CP2K| Program compiled at Fri Oct 3 18:03:43 CEST 2014
CP2K| Program compiled on dahu1.ee.ethz.ch
CP2K| Program compiled for iis_gcc_mkl
CP2K| Input file name pbscl_MD_251_01.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /home/yazdanin/cp2klne/cp2k141007/data/B
GLOBAL| Geminal file name BASIS_GEMINAL
GLOBAL| Potential file name /home/yazdanin/cp2klne/cp2k141007/data/G
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name /home/yazdanin/cp2klne/Examples/SS/Cl/25
GLOBAL| Method name CP2K
GLOBAL| Project name /home/yazdanin/cp2klne/Examples/SS/Cl/25
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. SL
GLOBAL| Run type MD
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| Total number of message passing processes 20
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 132052564 132052564 132052564 132052564
MEMORY| MemFree 130078312 130078312 130078312 130078312
MEMORY| Buffers 3956 3956 3956 3956
MEMORY| Cached 196856 196856 196856 196856
MEMORY| Slab 193260 193260 193260 193260
MEMORY| SReclaimable 95764 95764 95764 95764
MEMORY| MemLikelyFree 130374888 130374888 130374888 130374888
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K Developers Group (2000 - 2014) **
** **
*******************************************************************************
SCF PARAMETERS Density guess: RESTART
--------------------------------------------------------
max_scf: 30
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 1.00E-08
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
Outer loop SCF in use
No variables optimised in outer loop
eps_scf 1.00E-08
max_scf 100
No outer loop optimization
step_size 5.00E-01
MD| Molecular Dynamics Protocol
MD| Ensemble Type NVT
MD| Number of Time Steps 10000
MD| Time Step [fs] 10.00
MD| Temperature [K] 100.00
MD| Temperature tolerance [K] 0.00
MD| Print MD information every 1 step(s)
MD| File type Print frequency[steps] File names
MD| Coordinates 1 /home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl
MD| Velocities 1 /home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl
MD| Energies 1 /home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl
MD| Dump 1 /home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl
ROT| Rotational Analysis Info
ROT| Principal axes and moments of inertia in atomic units:
ROT| 1 2 3
ROT| EIGENVALUES 0.126902384E+11 0.127718032E+11 0.128540298E+11
ROT| X -0.164344194 0.984368760 -0.063317699
ROT| Y 0.985134938 0.160540560 -0.061121862
ROT| Z 0.050001393 0.072421501 0.996119966
ROT| Numer of Rotovibrational vectors: 6
Calculation of degrees of freedom
Number of atoms: 289
Number of Intramolecular constraints: 0
Number of Intermolecular constraints: 0
Invariants(translation + rotations): 6
Degrees of freedom: 861
Restraints Information
Number of Intramolecular restraints: 0
Number of Intermolecular restraints: 0
THERMOSTAT| Thermostat Info for PARTICLES
THERMOSTAT| Type of thermostat Canonical Sampling/Velocity Rescaling
THERMOSTAT| CSVR time constant [ fs] 15.00
THERMOSTAT| Initial Kinetic Energy 0.000000
THERMOSTAT| End of Thermostat Info for PARTICLES
************************** Velocities initialization **************************
Initial Temperature 100.00 K
COM velocity: 0.000000000000 -0.000000000000 -0.000000000000
COM position: 37.775406806626 38.025163966598 37.873075921796
Angular velocity: -0.000000108248 -0.000000058783 0.000000389404
*******************************************************************************
Number of electrons: 1502
Number of occupied orbitals: 751
Number of molecular orbitals: 751
Number of orbital functions: 3757
Number of independent orbital functions: 3757
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.01000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 271.1 0.00052785 -2241.0720508758 -2.24E+03
2 OT DIIS 0.15E+00 247.7 0.00032171 -2241.1593968668 -8.73E-02
3 OT DIIS 0.15E+00 103.9 0.00022657 -2241.2037791063 -4.44E-02
4 OT DIIS 0.15E+00 47.1 0.00014490 -2241.2344714047 -3.07E-02
5 OT DIIS 0.15E+00 40.4 0.00008881 -2241.2505580181 -1.61E-02
6 OT DIIS 0.15E+00 40.0 0.00005418 -2241.2567861682 -6.23E-03
7 OT DIIS 0.15E+00 39.1 0.00003371 -2241.2591462652 -2.36E-03
8 OT DIIS 0.15E+00 39.5 0.00002140 -2241.2600860535 -9.40E-04
9 OT DIIS 0.15E+00 38.8 0.00001543 -2241.2604336235 -3.48E-04
10 OT DIIS 0.15E+00 38.8 0.00001134 -2241.2606225089 -1.89E-04
11 OT DIIS 0.15E+00 39.0 0.00000750 -2241.2607374430 -1.15E-04
12 OT DIIS 0.15E+00 39.1 0.00000517 -2241.2607906795 -5.32E-05
13 OT DIIS 0.15E+00 38.9 0.00000374 -2241.2608155036 -2.48E-05
14 OT DIIS 0.15E+00 38.7 0.00000278 -2241.2608281489 -1.26E-05
15 OT DIIS 0.15E+00 38.7 0.00000205 -2241.2608353773 -7.23E-06
16 OT DIIS 0.15E+00 40.7 0.00000152 -2241.2608391165 -3.74E-06
17 OT DIIS 0.15E+00 39.0 0.00000114 -2241.2608411220 -2.01E-06
18 OT DIIS 0.15E+00 38.8 0.00000084 -2241.2608422538 -1.13E-06
19 OT DIIS 0.15E+00 39.8 0.00000063 -2241.2608428000 -5.46E-07
20 OT DIIS 0.15E+00 38.7 0.00000048 -2241.2608431038 -3.04E-07
21 OT DIIS 0.15E+00 38.2 0.00000037 -2241.2608432842 -1.80E-07
22 OT DIIS 0.15E+00 38.1 0.00000028 -2241.2608433881 -1.04E-07
23 OT DIIS 0.15E+00 38.5 0.00000022 -2241.2608434517 -6.36E-08
24 OT DIIS 0.15E+00 37.7 0.00000017 -2241.2608434888 -3.72E-08
25 OT DIIS 0.15E+00 38.4 0.00000013 -2241.2608435111 -2.22E-08
26 OT DIIS 0.15E+00 37.8 0.00000011 -2241.2608435246 -1.35E-08
27 OT DIIS 0.15E+00 38.1 0.00000009 -2241.2608435330 -8.35E-09
28 OT DIIS 0.15E+00 38.0 0.00000007 -2241.2608435391 -6.09E-09
29 OT DIIS 0.15E+00 37.8 0.00000005 -2241.2608435429 -3.86E-09
30 OT DIIS 0.15E+00 37.8 0.00000004 -2241.2608435453 -2.37E-09
*** SCF run NOT converged ***
Electronic density on regular grids: -1502.0000000000 0.0000000000
Core density on regular grids: 1501.9999996449 -0.0000003551
Total charge density on r-space grids: -0.0000003551
Total charge density g-space grids: -0.0000003551
Overlap energy of the core charge distribution: 0.00000000704752
Self energy of the core charge distribution: -5072.71212077156997
Core Hamiltonian energy: 1114.86935621966541
Hartree energy: 2221.14071272047840
Exchange-correlation energy: -504.55879172091301
Total energy: -2241.26084354529166
outer SCF iter = 1 RMS gradient = 0.42E-07 energy = -2241.2608435453
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.01000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 80.6 0.00000003 -2241.2608435468 -1.48E-09
2 OT DIIS 0.15E+00 38.0 0.00000003 -2241.2608435472 -4.17E-10
3 OT DIIS 0.15E+00 38.2 0.00000003 -2241.2608435476 -4.00E-10
4 OT DIIS 0.15E+00 37.8 0.00000002 -2241.2608435487 -1.09E-09
5 OT DIIS 0.15E+00 37.7 0.00000001 -2241.2608435489 -2.70E-10
6 OT DIIS 0.15E+00 37.8 5.1367E-09 -2241.2608435492 -2.29E-10
*** SCF run converged in 6 steps ***
Electronic density on regular grids: -1502.0000000000 0.0000000000
Core density on regular grids: 1501.9999996449 -0.0000003551
Total charge density on r-space grids: -0.0000003551
Total charge density g-space grids: -0.0000003551
Overlap energy of the core charge distribution: 0.00000000704752
Self energy of the core charge distribution: -5072.71212077156997
Core Hamiltonian energy: 1114.86935192034207
Hartree energy: 2221.14071682786471
Exchange-correlation energy: -504.55879153285713
Total energy: -2241.26084354917248
outer SCF iter = 2 RMS gradient = 0.51E-08 energy = -2241.2608435492
outer SCF loop converged in 2 iterations or 36 steps
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -2241.260843549192032
MD_ENERGIES| Initialization proceeding
******************************** GO CP2K GO! **********************************
INITIAL POTENTIAL ENERGY[hartree] = -0.224126084355E+04
INITIAL KINETIC ENERGY[hartree] = 0.136331400528E+00
INITIAL TEMPERATURE[K] = 100.000
INITIAL VOLUME[bohr^3] = 0.431893413318E+06
INITIAL CELL LNTHS[bohr] = 0.7558905E+02 0.7558905E+02 0.7558905E+02
INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.9000000E+02
******************************** GO CP2K GO! **********************************
14:33:23 NOTE in cp_output_handling:cp_print_key_unit_nr :: Writing
TRAJECTORY 1_0 to
/home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl_MD_251_01-pos-1.xyz
14:33:23 NOTE in cp_output_handling:cp_print_key_unit_nr :: Writing
VELOCITIES 1_0 to
/home/yazdanin/cp2klne/Examples/SS/Cl/251/01/pbscl_MD_251_01-vel-1.xyz
Number of electrons: 1502
Number of occupied orbitals: 751
Number of molecular orbitals: 751
Number of orbital functions: 3757
Number of independent orbital functions: 3757
Extrapolation method: PS Nth order
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.01000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 39.6 0.00012992 -2241.2412648215 -2.24E+03
2 OT DIIS 0.15E+00 37.9 0.00007885 -2241.2465219801 -5.26E-03
3 OT DIIS 0.15E+00 38.9 0.00005580 -2241.2490858546 -2.56E-03
4 OT DIIS 0.15E+00 38.9 0.00003574 -2241.2508007721 -1.71E-03
5 OT DIIS 0.15E+00 39.2 0.00002264 -2241.2517234086 -9.23E-04
6 OT DIIS 0.15E+00 38.7 0.00001396 -2241.2521134343 -3.90E-04
7 OT DIIS 0.15E+00 39.1 0.00000908 -2241.2522617018 -1.48E-04
8 OT DIIS 0.15E+00 38.0 0.00000579 -2241.2523257210 -6.40E-05
9 OT DIIS 0.15E+00 38.6 0.00000403 -2241.2523505892 -2.49E-05
10 OT DIIS 0.15E+00 38.1 0.00000288 -2241.2523636859 -1.31E-05
11 OT DIIS 0.15E+00 38.2 0.00000188 -2241.2523720407 -8.35E-06
12 OT DIIS 0.15E+00 38.3 0.00000131 -2241.2523755142 -3.47E-06
13 OT DIIS 0.15E+00 38.7 0.00000095 -2241.2523771210 -1.61E-06
14 OT DIIS 0.15E+00 38.1 0.00000070 -2241.2523779403 -8.19E-07
15 OT DIIS 0.15E+00 38.1 0.00000053 -2241.2523783767 -4.36E-07
16 OT DIIS 0.15E+00 38.5 0.00000039 -2241.2523786132 -2.37E-07
17 OT DIIS 0.15E+00 38.5 0.00000030 -2241.2523787338 -1.21E-07
18 OT DIIS 0.15E+00 38.1 0.00000022 -2241.2523788077 -7.39E-08
19 OT DIIS 0.15E+00 38.6 0.00000016 -2241.2523788471 -3.94E-08
20 OT DIIS 0.15E+00 38.0 0.00000012 -2241.2523788661 -1.90E-08
21 OT DIIS 0.15E+00 38.3 0.00000009 -2241.2523788785 -1.24E-08
22 OT DIIS 0.15E+00 38.8 0.00000007 -2241.2523788854 -6.94E-09
23 OT DIIS 0.15E+00 38.2 0.00000005 -2241.2523788892 -3.82E-09
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