Cube file with electron densities

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3 years 5 months ago #691 by philip
Hi

I'm interested in obtaining the electron density on a grid, similar to a cube file from gaussian, which is also implemented in a range of other ab initio programs such as dalton or psi4.

I have looked in the manual and there is no mention of this, so I assume it is not implemented. How difficult would it be to implement this, if I was to do it myself?

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3 years 5 months ago #692 by kallay
The densities are written to files DENSITY and DENSITY.SCF if keyword grdens is set, please see the description of grdens in the manual. If you are interested in an other format, you should hack the last lines of subroutine calcdens in dft.f.

Best regards,
Mihaly Kallay

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5 months 3 weeks ago #1216 by Skattejag
Good day,

I am a new user to MRCC.  I'm interested in obtaining the relaxed electron density information (via the 'fully relaxed CCSD density matrix') from CC calculations (eg. RHF CCSD/aug-cc-pVDZ), preferably in the format of a Gaussian .cube file. I would like to request assistance with the following:
Note: I am running the binary version of MRCC (March 18, 2022).

1) How can I convert the binary DENSITY and DENSITY.SCF files generated for a RHF CCSD/aug-cc-pVDZ calculation, obtained via the 'grdens=on' setting, to a human-readable ASCII file in the format given in the manual (see below)? Please bear in mind that I am not familiar with the Fortran programming language.

2) Are there other software (Interfaces?) that can read and convert these DENSITY files (and CCDENSITIES files) (see question 5 below)?

3) Regarding r1, w1, ρ1 (for example): Does the weight-1 value (w1) refer to the Becke weight at that point in space, used in the DFT numerical integration grids? If so, what is the significance or influence of this weight value on the reported electron density, gradient and/or Laplacian at a point in space, i.e. can this weight value be safely ignored - or does it need to be applied (multiplied?) to the density somehow in order to determine the correct final relaxed electron density at a point in space?

4) I see that the MRCC .out output (verbosity=3) does not mention that the relaxed density matrices are calculated when 'grdens=on' [only 'Components of dipole moment (unrelaxed)' is mentioned], or am I missing something (?). However, as stated in the manual "correlated calculations" will always yield relaxed electron densities obtained from "relaxed density matrices".
4a) Does the 'dens' keyword only affect the CCDENSITIES file and not the DENSITY file, whereas the 'grdens' keyword affects both the CCDENSITIES and DENSITY file?
4b) Will the values reported in CCDENSITIES be those of the relaxed or unrelaxed density matrices (does it depend on the keyword dens/grdens used)?

5) It is stated in the manual of the program Multiwfn (sobereva.com/multiwfn/), section 4.A.8 Analyze wavefunction higher than CCSD level (p.949-950), that Multiwfn can read the .molden and CCDENSITIES file of a CCSD-level calculation and 'convert the 1RDM into natural orbitals and save them to .molden file'. This generated MOLDEN.mwfn file will contain the natural orbitals of the CC wavefunction. Since it appears that it is required to set 'dens=1' and from the paragraph below, MultiWFN will analyse the one-particle density matrix stored in the CCDENSITIES file (and not the 2PDM since it is not present). Will I be able to determine the relaxed CC electron density from this file, by loading it in Multiwfn and producing an electron density Gaussian .cube file? 

According to the manual, for the 'dens' keyword: "If mod(dens,2)=1, only one-particle, if mod(dens,2)=0, both one- and twoparticle density matrices will be calculated and contracted with the available property
integrals." From the aforementioned 'dens=1' would result in only the one-particle density matrix being calculated and 'dens=2' would result in both one- and two-particle density matrices being determined and stored in the CCDENSITIES file(?).  

DENSITY file:
"   Ú       H    ]µÅÙߦ?e½:6ßìô¿¡™à#Tÿ¿Z&ª„ ?ßlõÁçl…?•¡Õä=–p?¬òý”µ†?Hdý†å?†«ðñÐT§?H   H   àæa䮼¨?ñ#œe ÷¿ÆÒrN´Óö¿–,idö?&ÑH­;“?¸GE&“f? VëŽõGš?ÔÉÍKkü˜?jþ+æÚV¸?H   H   àŠ€mÖÞ¨?÷cüPçÜô¿9/p6÷¿†Ö™†ñ…?äïڂÖ?”^¹¡Þw?.‘VBž?9שb€Ÿ?Ôíþ Ý{¼?H   H   €ÀP•Kè¸?F\KYô¿_g|qgEÀð…›G¿¬™?.¢™Žks?“Dô…E†e?&)lFMyp?T5Fu‡,~?F¬tj?H   H   ÀÚå6¹?’ÇÎ<8²÷¿¼ÜŽš¹ü¿î”Üm(Ñ0?ŒºZýr§†?¥ŽGðm?»K©k?‹‹?{\ç'?qaà*Ð_©?H   H   @Qó@œ¿?l÷04DTø¿£Øæ’ø¿áàNc0? §R”ø?º™%A¥Kp?BôÛê=–?ª‡’À?”?KŠãbì³?H   H    "ã¹»êÀ?
,††ó¿*òµSbý¿ÚëMìŒ?    ¡H±o?R~˯RH~? W ©9£?Q)éЋ:–?–Ö:/—l°?H   H   8†!»..."

From MRCC manual:


Thank you for your assistance with this matter.
Kind regards
Cameron
 
 

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2 months 2 days ago #1259 by SteveCoyMR
One convenient approach to electron density and electron density difference.
1. Use ORBKIT to convert the MOLDEN file to a cube file (1PDM form). Orbkit allows the selection of alpha or beta spins in UHF runs separately and allows definition of the volume. Multiwfn makes spin selection more difficult.
2. use cube_tools (github.com/funkymunkycool/Cube-Toolz) for cube file arithmetic.
3. Use VMD or Gabedit for visualization of the cube data.

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