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#1 2019-02-17 01:57:34

NickD
Member
Registered: 2019-01-24
Posts: 16

Electron density difference using cube files

Hello

I am trying to get the electron density difference using cube files. I have sent the cube files via email. I use Multiwfn 3.6 and I get the following error.


Selected file: Z:\Documents\CRYSTAL\MoS2\MoS2-1water1.cube
Please wait...
Title line of this file:
  Charge density
    23.17594863    23.17120766   944.86306696    90.000000  90.000000 120.00460

Total number of atoms:      51
Translation vector:        X           Y           Z     (Bohr)
          Vector 1:     0.234100    0.000005    0.000000
          Vector 2:    -0.117047    0.202684    0.000000
          Vector 3:     0.000000    0.000000    0.234156
The range of x is from     0.000000 to    23.175900 Bohr,  100 points
The range of y is from     0.000000 to    20.065716 Bohr,  100 points
The range of z is from    -2.502575 to     8.268601 Bohr,   47 points
Total number of grid points:    470000
This grid data will take up at least     3 MB memory

Loading grid data, please wait...

The minimum value: -0.16919000E-02 at   15.450600    6.485888    0.307297 Bohr
The maximum value:  0.10483000E+04 at   13.577800    8.310044   -2.502575 Bohr
Differential element:   0.0111103098 Bohr^3
Summing up positive value in grid file:                60433.3860325755
After multiplied by differential element:                671.4336439982
Summing up negative value in grid file:                   -0.0084385100
After multiplied by differential element:                 -0.0000937545
Summing up all value in grid file:                     60433.3775940655
After multiplied by differential element:                671.4335502437

Loaded Z:\Documents\CRYSTAL\MoS2\MoS2-1water1.cube successfully!
Formula: H2 O1 S32 Mo16
Molecule weight:      2579.45528

Note: A set of grid data presents in memory
                    ************ Main function menu ************
0 Show molecular structure and view isosurface
1 Output all properties at a point
2 Topology analysis
3 Output and plot specific property in a line
4 Output and plot specific property in a plane
5 Output and plot specific property within a spatial region (calc. grid data)
6 Check & modify wavefunction
7 Population analysis and atomic charges
8 Orbital composition analysis
9 Bond order analysis
10 Plot Total/Partial/Overlap population density-of-states (DOS)
11 Plot IR/Raman/UV-Vis/ECD/VCD/ROA spectrum
12 Quantitative analysis of molecular surface
13 Process grid data
14 Adaptive natural density partitioning (AdNDP) analysis
15 Fuzzy atomic space analysis
16 Charge decomposition analysis (CDA) and extended CDA (ECDA)
17 Basin analysis
18 Electron excitation analysis
19 Orbital localization analysis
20 Visual study of weak interaction
21 Energy decomposition analysis
100 Other functions (Part1)        200 Other functions (Part2)
13

                   ============= Process grid data ==============
-2 Visualize isosurface of present grid data
-1 Return to main menu
0 Output present grid data to Gaussian cube file
1 Output all data points with value and coordinate
2 Output data points in a XY plane by specifying Z
3 Output data points in a YZ plane by specifying X
4 Output data points in a XZ plane by specifying Y
5 Output average data of XY planes in a range of Z
6 Output average data of YZ planes in a range of X
7 Output average data of XZ planes in a range of Y
8 Output data points in a plane defined by three atom indices
9 Output data points in a plane defined by three points
10 Output data points in specified value range
11 Grid data calculation
12 Map values of a cube file to specified isosurface of present grid data
13 Set value of the grid points that far away from / close to some atoms
14 Set value of the grid points outside overlap region of two fragments
15 If data value is within certain range, set it to a specified value
16 Scale data range
17 Show statistic data of the points in specific spatial and value range
18 Calculate and plot integral curve in X/Y/Z direction
11
                --------------- Grid data calculation ------------
0 Return
1 Add a constant                       e.g. A+0.1=C
2 Add a grid file                      i.e. A+B=C
3 Subtract a constant                  e.g. A-0.1=C
4 Subtract a grid file                 i.e. A-B=C
5 Multiplied by a constant             e.g. A*0.1=C
6 Multiplied by a grid file            i.e. A*B=C
7 Divided by a constant                e.g. A/5.2=C
8 Divided by a grid file               i.e. A/B=C
9 Exponentiation                       e.g. A^1.3=C
10 Square sum with a grid file         i.e. A^2+B^2=C
11 Square subtract with a grid file    i.e. A^2-B^2=C
12 Get average with a grid file        i.e. (A+B)/2=C
13 Get absolute value                  i.e. |A|=C
14 Get exponential value with base 10  i.e. 10^A=C
15 Get logarithm with base 10          i.e. log10(A)=C
16 Get natural exponential value       i.e. e^A=C
17 Get natural logarithm               i.e. ln(A)=C
18 Add a grid file multiplied by a value  i.e. A+0.4*B=C
19 The same as 6 but with weighting function min(|A|,|B|)/max(|A|,|B|)
20 Multiplied by a coordinate variable
21 Get minimal value with another function    i.e. min(A,B)
22 Get min(|A|,|B|)
4
Input another .cub or .grd file name
MoS2-1water1-slab.cube
Error: The grid setting of this cube file is inconsistent with that of the grid data stored in memory!

The first file contains slab+water, the second only the slab, and the third only the water.

Thank you.

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#2 2019-02-17 02:29:01

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 1,100
Website

Re: Electron density difference using cube files

Dear NickD,

In order to get difference between cube files, the number of grid points (as well as grid positions) of the files must be identical. You can use Multiwfn to load the two cube files respectively and compare below section

Translation vector:        X           Y           Z     (Bohr)
          Vector 1:     0.234100    0.000005    0.000000
          Vector 2:    -0.117047    0.202684    0.000000
          Vector 3:     0.000000    0.000000    0.234156
The range of x is from     0.000000 to    23.175900 Bohr,  100 points
The range of y is from     0.000000 to    20.065716 Bohr,  100 points
The range of z is from    -2.502575 to     8.268601 Bohr,   47 points

The two files must differ in this section, this is why the calculation was failed

Best,

Tian

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#3 2019-02-17 02:47:55

NickD
Member
Registered: 2019-01-24
Posts: 16

Re: Electron density difference using cube files

Hi Tian

Thank you for your quick reply. I am trying to plot Delta rho = rho(slab+water)- rho(slab)-rho(water). So I do have one structure for slab+water, where I calculate rho(slab+water). Using the same structure I remove the water molecule and thus I obtain rho(slab). In a similar fashion I obtain rho(water). All files are cube files, but will have different grid ranges although their grids are the same (100x100x47). Any ideas how to handle this ?

Thank again,

Nick

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#4 2019-02-17 02:50:51

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 1,100
Website

Re: Electron density difference using cube files

Dear Nick,

I am not familiar with CRYSTAL program, if there are options used to set original point and translation vectors of the grid points, for the three systems this setting should be set to identical.

Tian

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#5 2019-02-17 02:55:46

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 1,100
Website

Re: Electron density difference using cube files

I forgot to mention that your .cube file cannot be properly processed by Multiwfn, because only cubic grid is supported by current version of Multiwfn, however the three translation vectors of your cube file are not all parallel to the three Cartesian axes.
I intend to extend Multiwfn to make Multiwfn support triclinic grid in the future.

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