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How to visualise the total electron density from a Gaussian 16 calculation?
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Mark Evenett
How to visualise the total electron density from a Gaussian 16 calculation?
When GaussView gives you the error
Surface build failed! Processing mesh, No data to plot. IsoValue may be out of range
it means that the data in your .cube file doesn't have values of density at that isovalue. So when it tries to plot a surface, it cannot plot anything.
The IsoValue (default is 0.00040, I believe) means that you construct a surface at every place in the density where the density equals the IsoValue ('iso' = 'same'). So for the default, it opens up your .cube file and looks for the cube coordinates that have density at (or near) 0.00040, and plots a surface that connects these points (this is your 'mesh').
Most likely, your density values are too small large to plot an isosurface at this value. Try making the default density isovalue in GaussView to be something smaller larger and go from there. (Practically, I'd keep shifting an order of magnitude until a surface builds, e.g. try a value of 0.004 next).
Even better, you should look into the .cube file itself to see what your volumetric data looks like. The first few lines define the grid spacing and dimensions of the cube, but then you will see a bunch of floating point values. Here's an example .cube I took from this site (also a good reference):
CPMD CUBE FILE.
OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
3 0.000000 0.000000 0.000000
40 0.283459 0.000000 0.000000
40 0.000000 0.283459 0.000000
40 0.000000 0.000000 0.283459
8 0.000000 5.570575 5.669178 5.593517
1 0.000000 5.562867 5.669178 7.428055
1 0.000000 7.340606 5.669178 5.111259
-0.25568E-04 0.59213E-05 0.81068E-05 0.10868E-04 0.11313E-04 0.35999E-05
: : : : : :
: : : : : :
: : : : : :
In this case there will be 40 x 40 x 40 floating point values
: : : : : :
: : : : : :
: : : : : :
Look at the value of your floating point numbers at the end. As a starting point, pick a number for your isovalue that is about an order of magnitude less than your largest values, and adjust from there.
If your values are all at or near zero (so, practically speaking, on the order of 1E-8 or lower) then you need to revisit how you are generating the .cube file, since your cube is not capturing any density---then it's a cubegen issue not an isosurface issue.
Surface build failed! Processing mesh, No data to plot. IsoValue may be out of range
it means that the data in your .cube file doesn't have values of density at that isovalue. So when it tries to plot a surface, it cannot plot anything.
The IsoValue (default is 0.00040, I believe) means that you construct a surface at every place in the density where the density equals the IsoValue ('iso' = 'same'). So for the default, it opens up your .cube file and looks for the cube coordinates that have density at (or near) 0.00040, and plots a surface that connects these points (this is your 'mesh').
Most likely, your density values are too small large to plot an isosurface at this value. Try making the default density isovalue in GaussView to be something smaller larger and go from there. (Practically, I'd keep shifting an order of magnitude until a surface builds, e.g. try a value of 0.004 next).
Even better, you should look into the .cube file itself to see what your volumetric data looks like. The first few lines define the grid spacing and dimensions of the cube, but then you will see a bunch of floating point values. Here's an example .cube I took from this site (also a good reference):
CPMD CUBE FILE. OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z 3 0.000000 0.000000 0.000000 40 0.283459 0.000000 0.000000 40 0.000000 0.283459 0.000000 40 0.000000 0.000000 0.283459 8 0.000000 5.570575 5.669178 5.593517 1 0.000000 5.562867 5.669178 7.428055 1 0.000000 7.340606 5.669178 5.111259 -0.25568E-04 0.59213E-05 0.81068E-05 0.10868E-04 0.11313E-04 0.35999E-05 : : : : : : : : : : : : : : : : : : In this case there will be 40 x 40 x 40 floating point values : : : : : : : : : : : : : : : : : :
Look at the value of your floating point numbers at the end. As a starting point, pick a number for your isovalue that is about an order of magnitude less than your largest values, and adjust from there.
If your values are all at or near zero (so, practically speaking, on the order of 1E-8 or lower) then you need to revisit how you are generating the .cube file, since your cube is not capturing any density---then it's a cubegen issue not an isosurface issue.
When GaussView gives you the error
it means that the data in your
.cubefile doesn't have values of density at that isovalue. So when it tries to plot a surface, it cannot plot anything.The IsoValue (default is
0.00040, I believe) means that you construct a surface at every place in the density where the density equals the IsoValue ('iso' = 'same'). So for the default, it opens up your.cubefile and looks for the cube coordinates that have density at (or near)0.00040, and plots a surface that connects these points (this is your 'mesh').Most likely, your density values are too
smalllarge to plot an isosurface at this value. Try making the default density isovalue in GaussView to be somethingsmallerlarger and go from there. (Practically, I'd keep shifting an order of magnitude until a surface builds, e.g. try a value of0.004next).Even better, you should look into the
.cubefile itself to see what your volumetric data looks like. The first few lines define the grid spacing and dimensions of the cube, but then you will see a bunch of floating point values. Here's an example.cubeI took from this site (also a good reference):Look at the value of your floating point numbers at the end. As a starting point, pick a number for your isovalue that is about an order of magnitude less than your largest values, and adjust from there.
If your values are all at or near zero (so, practically speaking, on the order of
1E-8or lower) then you need to revisit how you are generating the.cubefile, since your cube is not capturing any density---then it's acubegenissue not an isosurface issue.When GaussView gives you the error
it means that the data in your
.cubefile doesn't have values of density at that isovalue. So when it tries to plot a surface, it cannot plot anything.The IsoValue (default is
0.00040, I believe) means that you construct a surface at every place in the density where the density equals the IsoValue ('iso' = 'same'). So for the default, it opens up your.cubefile and looks for the cube coordinates that have density at (or near)0.00040, and plots a surface that connects these points (this is your 'mesh').Most likely, your density values are too
smalllarge to plot an isosurface at this value. Try making the default density isovalue in GaussView to be somethingsmallerlarger and go from there. (Practically, I'd keep shifting an order of magnitude until a surface builds, e.g. try a value of0.004next).Even better, you should look into the
.cubefile itself to see what your volumetric data looks like. The first few lines define the grid spacing and dimensions of the cube, but then you will see a bunch of floating point values. Here's an example.cubeI took from this site (also a good reference):Look at the value of your floating point numbers at the end. As a starting point, pick a number for your isovalue that is about an order of magnitude less than your largest values, and adjust from there.
If your values are all at or near zero (so, practically speaking, on the order of
1E-8or lower) then you need to revisit how you are generating the.cubefile, since your cube is not capturing any density---then it's acubegenissue not an isosurface issue.More
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