Convergence problem in MD NVT calculation DFT. Tutorials do not work. Help please.
Glaucio
glau... at gmail.com
Sun Mar 6 16:28:21 UTC 2016
Dear. I'm new user cp2k, I need to simulate vibrational spectra of molecular
dynamics and used the tutorials working with TRAVIS program. Unfortunately
already I made several efforts according to several posts made, but I can
not simulate a simple spectrum of a water molecule. Could anyone help me to
see if there is something to do in the input to improve the outcome. What I
observe is a molecule finds rotation around its own axis. I am sending
attached files and graphs obtained.
Thank you for your help.
glaucio
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Command line:
"travis -p agua_wannier_BLYP.xyz"
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TRajectory Analyzer and VISualizer - Open-source freeware under GNU GPL v3
Copyright (c) Martin Brehm (2009-2014)
Martin Thomas (2012-2014)
Barbara Kirchner (2009-2014)
University of Leipzig / University of Bonn.
http://www.travis-analyzer.de
Please cite:
M. Brehm and B. Kirchner, J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.
There is absolutely no warranty on any results obtained from TRAVIS.
# Running on mark11.ufrj.com at Sun Mar 6 13:12:12 2016 (PID 11939).
# Running in /usr/local/gqt/rodacp2k/exemplo_metanol_travis/raman
# Source code version: Jan 17 2014.
# Compiled at Jan 19 2014 05:12:11.
# Compiler version: 4.8.2
# Target platform: Linux
# Compile flags: DEBUG_ARRAYS
# Machine: int=4b, long=8b, addr=8b, 0xA0B0C0D0=D0,C0,B0,A0.
# User home: /home/glaucio
# Exe path: /usr/bin/travis
# Input from terminal, Output to terminal
>>> Please use a color scheme with dark background or specify "-nocolor"! <<<
Loading configuration from /home/glaucio/.travis.conf ...
[Renaming existing File input.txt to #7#input.txt ...OK.]
Opening position trajectory agua_wannier_BLYP.xyz ...
Trajectory contains approximately 1791 time steps (file size 885.07 KB).
No element data found for atom "X".
7 atoms in the system: 2x H, 1x O, 4x X
System extent: X = { -26 .. +26 pm }, dX = 53 pm
(in step 1) Y = { -76 .. +76 pm }, dY = 151 pm
Z = { -20 .. +52 pm }, dZ = 72 pm
*** Interactive query of settings ***
Unrecognized atom types: X
Possibly, atom type "X" are Wannier centers. If so, do not assign data to them.
Do you want to assign atom data to them (y/n)? [no]
The advanced mode includes some options which are quite powerful,
yet possibly weird or seldomly required. This includes support for
NPT ensemble, non-periodic systems, user-definded virtual atoms, pseudomolecules, ...
Use the advanced mode up to the function selection menu (y/n)? [no]
A cell vector of 310.46 pm would result in a density of 1.0 g/cm^3.
Are the 3 cell vectors of the same size (yes/no)? [yes]
Enter length of cell vector in pm: 1000
The box size is 1000.00 x 1000.00 x 1000.00 pm.
The overall box density is 0.029924 g/cm^3.
Atom type "X" has bond radius 0. Exclude it from the system (y/n)? [yes]
Molecule recognition [###]
1 molecules found.
Sorting atom types...
Setting up bond lists...
Building atom codes...
Creating topological atom order...
Creating bond list...
Creating angle list...
Grouping together equivalent molecules...
Found 1 unique molecule types.
Sorting molecule types by molecular mass...
Found 0 rings.
Molecule recognition finished.
Uniting molecules which have been broken by wrapping...
*** The following 1 kind of molecules has been recognized:
(ordered by molecular mass)
- Molecule 1: H2O (1 piece, 18.02 g/mol)
(2 noneq. atoms, 1 noneq. bond, 1 noneq. angle)
Accept these molecules (y) or change something (n)? [yes]
Output of bond matrices:
*** Molecule 1: H2O; Representant 1; Distances in pm ***
H1 H2 O1
H1 *** - 96
H2 - *** 96
O1 96 96 ***
Atoms H1, H2 are equivalent.
You can create images of the structural formulas with the atom labels for easier
identification of the atoms (requires installed GraphViz package - see www.graphviz.org).
Create images of the structural formulas (y/n)? [no]
The atoms are currently ordered by topological priority.
Defining virtual atom #1 as molecular Center of Geometry:
- H2O...
Defining virtual atom #2 as molecular Center of Mass:
- H2O...
>>> 2 virtual atoms have been defined: >>>
#1 in H2O: Center of Geometry.
#2 in H2O: Center of Mass.
<<< End of virtual atoms <<<
>>> List of functions <<<
*** Static (time independent) Functions
cdf - Combined Distribution Function
rdf - Radial Distribution Function
adf - Angular Distribution Function
ddf - Dihedral Distribution Function
pldf - Point-Plane Distance Distribution
lidf - Point-Line Distance Distribution
plproj - Plane Projection Distribution
dprof - Fixed Plane Density Profile
dens - Density Distribution Function
sdf - Spatial Distribution Function
psdf - Pseudo SDF (only 2 ref. atoms)
dip - Dipole Distribution Function
cond - Evaluate structural condition
*** Dynamic (time dependent) Functions
vdf - Velocity Distribution Function
msd - Mean Square Displacement / Diffusion Coefficients
acf - Velocity Autocorrelation Functions
rdyn - Vector Reorientation Dynamics
vhcf - Van Hove Correlation Function
aggr - Aggregation Functions (DACF, DLDF, DDisp)
*** Spectroscopic Functions
power - Calculate Power Spectrum
ir - Calculate IR Spectrum
raman - Calculate Raman Spectrum
*** Miscellaneous Functions
env - Save trajectory of RM environment / TDO Plot
proc - Save processed Trajectory
cut - Cut Clusters
reg - Region-specific Analysis
(You may specify multiple analyses at once, but
the safe way is to perform only one kind of analysis at a time.)
Which functions to compute (comma separated)? ir
ir - Calculate IR Spectrum
The advanced mode includes some options which are quite powerful,
yet possibly weird or seldomly required.
Use the advanced mode for the main part (y/n)? [no]
Enter the length of one trajectory time step in fs: [0.5]
Compute IR spectrum of whole system (y/n)? [yes]
Compute also IR spectra for certain molecule types (y/n)? [no]
*** Definition of system-wide IR spectrum ***
>>> Infrared Spectrum >>>
>>> Dipole definition >>>
TRAVIS can calculate dipole moments either from wannier centers (you need
to have those in the trajectory then) or from fixed atomic partial charges.
Obtain dipole vectors from wannier centers (y/n)? [yes]
Atom type X is excluded from system, probably the wannier centers.
Which atom label do the wannier centers have (H, O, X)? [X]
Enter the negative charge of the wannier centers (without sign): [2.0]
Enter core charge (mind pseudopotentials!) for atom type H: [1.0]
Enter core charge (mind pseudopotentials!) for atom type O: [6.0]
- Wannier center 4 belongs to H2O[1] O1 (30 pm).
- Wannier center 5 belongs to H2O[1] H1 (44 pm).
- Wannier center 6 belongs to H2O[1] O1 (30 pm).
- Wannier center 7 belongs to H2O[1] H2 (44 pm).
- Molecule H2O contains 4 wannier centers. Total charge is 8.00 - 8.00 = 0.00
- H2O: Dipole reference point is #1.
Calculating dipole moments from first time step...
- H2O: Min. 1.8508, Max. 1.8508, Avg. 1.8508 Debye.
Cartesian dipole vector is ( 9.56247E-07 | 0 | 1.8508 ).
<<< End of Dipole definition <<<
Hint: The resolution of the ACF may never be higher than the number of processed steps.
Suggested is 75 percent of the processed steps, but not more than approx. 16384.
Enter the resolution (=depth) of the dipole ACF (in time steps): [1343]
CalcFFTSize(): 1343 = 2^1 * 3^3 * 5^2 - 7. Prime factors other than 2, 3, 5 not allowed.
The next "fast" size for FFT is 1350. Using this instead of 1343 as depth.
This corresponds to a spectral resolution of 24.7085 cm^-1.
A time step length of 0.5 fs allows a spectral range up to 33356.4 cm^-1.
Calculate spectrum up to which wave number (cm^-1)? [5000.0 cm^-1]
CalcFFTSize(): 5400 = 2^3 * 3^3 * 5^2. All prime factors within 2, 3, 5. Fine.
Zero padding increases the spectral resolution to 6.1771 cm^-1.
Convert intensity axis of spectrum to decibel (y/n)? [no]
ACF: Trying to reserve 21.09 KB of memory...
<<< End of Infrared Spectrum <<<
Not wrapping molecules into the box.
Not removing center of mass movement of the box.
Skip repeated time steps (y/n)? [no]
In which time step to start processing the trajectory? [1]
How many time steps to use (from this position on)? [all]
Use every n-th time step from the trajectory? [1]
Using 1791 time steps: Every 1st within range 1 - approx. 1791.
########## All information collected ##########
>>> Initialization >>>
Creating global IR Spectrum...
RDyn Cache: Trying to allocate 21.69 KB of memory...
<<< End of Initialization <<<
### Starting Main Analysis ###
Hint: Press CTRL+C once to softly interrupt analysis and still write the results.
Creating an empty file named EXIT ("touch EXIT") has the same effect.
Step 0 ..................................................
Step 50 ..................................................
Step 1050 .....................................
End of trajectory file reached.
########## Analysis finished ##########
1781 time steps processed.
*** Global IR Spectrum
Deriving vectors (1st derivative)...
[#]
Autocorrelating cached vectors...
[#]
1493775 bin entries.
Saving result as rdyn_[dip_global].csv ...
[Renaming existing File rdyn_[dip_global].csv to #7#[...].csv ...OK.]
Creating reorientation spectrum:
Saving ACF as acf_[dip_global].d1.csv ...
[Renaming existing File acf_[dip_global].d1.csv to #7#[...].csv ...OK.]
Mirroring ACF...
Saving mirrored ACF as acf_[dip_global].d1.m.csv ...
[Renaming existing File acf_[dip_global].d1.m.csv to #7#[...].csv ...OK.]
Applying window function to ACF...
Saving windowed ACF as acf_[dip_global].d1.w.csv ...
[Renaming existing File acf_[dip_global].d1.w.csv to #7#[...].csv ...OK.]
Performing fourier transformation...
Saving spectrum as spectrum_[dip_global].d1.csv ...
[Renaming existing File spectrum_[dip_global].d1.csv to #7#[...].csv ...OK.]
Note: To show a list of all persons which contributed to TRAVIS,
please add "-credits" to your command line arguments, or set the
variable "SHOWCREDITS" to "TRUE" in your travis.conf file.
Source code from other projects used in TRAVIS:
- lmfit from Joachim Wuttke
- kiss_fft from Mark Borgerding
- voro++ from Chris Rycroft
http://www.travis-analyzer.de
Please cite:
* "TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories",
M. Brehm, B. Kirchner; J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.
* "Computing Vibrational Spectra from ab initio Molecular Dynamics",
M. Thomas, M. Brehm, R. Fligg, P. Voehringer, B. Kirchner; Phys. Chem. Chem. Phys. 2013, 15, pp 6608-6622.
*** The End ***
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