Charge Density Difference plotting
Posted: Thu Sep 03, 2009 9:53 am
Dear List,
I have been working with dissociation of methane on Ni(111) with VASP as my DFT code in conjunction with your scripts.
Recently, I made a plot of the electron density difference plot (EDD) with your scripts (am a Newbie in this field).
As a first test, I made an EDD plot of the He2 [dihelium] molecule and I got a good plot with your scripts.
Where I used to get the EDD_CHGCAR via,
[He-He] – ([He’]+[He’’])
Where I used your,
* chgsum.pl for ([He’]+[He’’]) CHGCAR file
* chgdiff.pl for [He-He] – ([He’]+[He’’]) i.e. to get the final EDD CHGCAR file.
Here, [He-He] = dihelium CHGCAR from VASP,
[He’], [He’’] are the CHGCAR files from the individual He atoms.
- - -
Then, I applied the same method for the EDD of my CH3-H/Ni(111), transition state (TS), but I got a very dimmed picture! Where I see no bonding-contours say, for the CH3-Ni(atop) and H-Ni atoms etc. Only C-H bonds are strong enough to see.
In this case also, I made the EDD_CHGCAR via,
[CH3-H/Ni(111)] – ([CH3-H]+[Ni(111)]) and used the .pl scripts which I described above,
Question:
Is it the correct way of plotting EDD in this TS?
Please note that,
Since, [CH3-H/Ni(111)] has 17 atoms (5+12) and [CH3-H] has 5, and [Ni(111)] has 12 atoms in their supercell, Does this kind of ordering make any alternation in the EDD matrix elements in the final CHGCAR file ? In other words, do I want to plot only some parts in the final CHGCAR file?
For the plotting I used: VEND
http://www.geocities.jp/kmo_mma/crystal/en/vesta.html
Furthermore, I used quite tight criteria in the INCAR file as shown below with a TS geometry.
I hope some experienced person with EDD plotting can easily give a reply!
With thanks in advance
Krishna Mohan G P
Theor
University of Leiden.
--------------------------------------------------------------------
INCAR ==
SYSTEM = NI-fcc-zRELAX
EDIFF = 1E-8
GGA=91
VOSKOWN=1
ISPIN=2
LREAL=.FALSE.
ADDGRID = .TRUE.
PREC= Accurate
ENCUT =450 eV
ISMEAR=-1
SIGMA=0.1
IDIPOL=3
NGX = 42
NGY = 42
NGZ = 168
NGXF= 84
NGYF= 84
NGZF= 336
--------------------------------------------------------------------
Ni.ch4/POSCAR ==
Ni FCC CartesianSlab 20 Box,3.52 INI OPT AVG
1.0
4.3111019474 -2.4890158698 0.0000000000
4.3111019474 2.4890158698 0.0000000000
0.0000000000 0.0000000000 20.000000000
12 1 4
Cartesian
0.000000000 0.000000000 0.0000000
2.155550973 -1.244507934 0.0000000
2.155550973 1.244507934 0.0000000
4.311101947 0.000000000 0.0000000
1.437033984 0.000000000 -2.005000
3.592584957 -1.244507935 -2.005000
3.592584957 1.244507935 -2.005000
5.748135931 0.000000000 -2.005000
2.874067963 0.000000000 -4.010000
5.029618915 -1.244507947 -4.010000
5.029618915 1.244507947 -4.010000
7.185169910 0.000000000 -4.010000
-0.03813187 0.00000000 2.12680810
0.54419159 0.90843506 2.31474047
0.54419159 -0.90843506 2.31474047
-0.91861056 0.00000000 2.78125050
-1.19719641 0.00000000 1.04061129
--------------------------------------------------------------------
KPOINTS ==
K-points
0
Gamma
11 11 1
0. 0. 0.
I have been working with dissociation of methane on Ni(111) with VASP as my DFT code in conjunction with your scripts.
Recently, I made a plot of the electron density difference plot (EDD) with your scripts (am a Newbie in this field).
As a first test, I made an EDD plot of the He2 [dihelium] molecule and I got a good plot with your scripts.
Where I used to get the EDD_CHGCAR via,
[He-He] – ([He’]+[He’’])
Where I used your,
* chgsum.pl for ([He’]+[He’’]) CHGCAR file
* chgdiff.pl for [He-He] – ([He’]+[He’’]) i.e. to get the final EDD CHGCAR file.
Here, [He-He] = dihelium CHGCAR from VASP,
[He’], [He’’] are the CHGCAR files from the individual He atoms.
- - -
Then, I applied the same method for the EDD of my CH3-H/Ni(111), transition state (TS), but I got a very dimmed picture! Where I see no bonding-contours say, for the CH3-Ni(atop) and H-Ni atoms etc. Only C-H bonds are strong enough to see.
In this case also, I made the EDD_CHGCAR via,
[CH3-H/Ni(111)] – ([CH3-H]+[Ni(111)]) and used the .pl scripts which I described above,
Question:
Is it the correct way of plotting EDD in this TS?
Please note that,
Since, [CH3-H/Ni(111)] has 17 atoms (5+12) and [CH3-H] has 5, and [Ni(111)] has 12 atoms in their supercell, Does this kind of ordering make any alternation in the EDD matrix elements in the final CHGCAR file ? In other words, do I want to plot only some parts in the final CHGCAR file?
For the plotting I used: VEND
http://www.geocities.jp/kmo_mma/crystal/en/vesta.html
Furthermore, I used quite tight criteria in the INCAR file as shown below with a TS geometry.
I hope some experienced person with EDD plotting can easily give a reply!
With thanks in advance
Krishna Mohan G P
Theor
University of Leiden.
--------------------------------------------------------------------
INCAR ==
SYSTEM = NI-fcc-zRELAX
EDIFF = 1E-8
GGA=91
VOSKOWN=1
ISPIN=2
LREAL=.FALSE.
ADDGRID = .TRUE.
PREC= Accurate
ENCUT =450 eV
ISMEAR=-1
SIGMA=0.1
IDIPOL=3
NGX = 42
NGY = 42
NGZ = 168
NGXF= 84
NGYF= 84
NGZF= 336
--------------------------------------------------------------------
Ni.ch4/POSCAR ==
Ni FCC CartesianSlab 20 Box,3.52 INI OPT AVG
1.0
4.3111019474 -2.4890158698 0.0000000000
4.3111019474 2.4890158698 0.0000000000
0.0000000000 0.0000000000 20.000000000
12 1 4
Cartesian
0.000000000 0.000000000 0.0000000
2.155550973 -1.244507934 0.0000000
2.155550973 1.244507934 0.0000000
4.311101947 0.000000000 0.0000000
1.437033984 0.000000000 -2.005000
3.592584957 -1.244507935 -2.005000
3.592584957 1.244507935 -2.005000
5.748135931 0.000000000 -2.005000
2.874067963 0.000000000 -4.010000
5.029618915 -1.244507947 -4.010000
5.029618915 1.244507947 -4.010000
7.185169910 0.000000000 -4.010000
-0.03813187 0.00000000 2.12680810
0.54419159 0.90843506 2.31474047
0.54419159 -0.90843506 2.31474047
-0.91861056 0.00000000 2.78125050
-1.19719641 0.00000000 1.04061129
--------------------------------------------------------------------
KPOINTS ==
K-points
0
Gamma
11 11 1
0. 0. 0.