Posts by prasanta13

prasanta13 · Quantum Chemistry

Sorry for the late reply, I am incredibly sorry.
I have asked the PSI4 community to extract 2PDM at CCSD(T) level. However, I got nothing yet. Could you tell me how to obtain the 2PDM from the CCSD(T) calculation from PSI4 (preferred since I can access it) or Molpro.

Thanking You
Prasanta

prasanta13 · Quantum Chemistry

Many many thanks Prof Tian. I am working with PSI4, Lets see if I can find something.

prasanta13 · Quantum Chemistry

Hi Prof Tian,
I am trying to obtain the HF and CCSD(T) one and two-particle density matrix from the respective wavefunction (like HF or Correlated). I can do this using PySCF, but it takes a lot of memory (1TB for ~200 basis functions for CCSD(T)). This is why I tried to do it with other programs like Psi4 or ORCA which are less memory hungry. However, I do not know how to obtain the DM from wfn file. Note: I am using a custom basis functions.
Thanks
Prasanta

prasanta13 · Multiwfn and wavefunction analysis

Thank you, Prof. TIan. It works.....

prasanta13 · Multiwfn and wavefunction analysis

Prof. Tian, In case someone wants to do the same thing you mentioned in the 2nd point of your answer, the manual is not clear (v3.8). I want a set of orbitals suppose homo, lumo, homo+-2 and lumo+-2 into different cube files. how can one proceed?

prasanta13 · Multiwfn and wavefunction analysis

Thank You Prof. Tian...

prasanta13 · Multiwfn and wavefunction analysis

Thank you, Professor Tian. I get that part. Can you please tell me what the following means?
139a -> 141a : 0.380347 (c= -0.61672301)
orb pairs config coeff ??
I get orbital pairs, but the next two numbers bothers me. What are these?

prasanta13 · Multiwfn and wavefunction analysis

Dear Prof Tian,
I have performed vertical excitation using ORCA (default setting) with RSH/def2-TZVP.
The output is this, (only printing interesting texts)
STATE 1: E= 0.085477 au 2.326 eV 18760.0 cm**-1 = 0.000000
139a -> 141a : 0.380347 (c= -0.61672301)
139a -> 142a : 0.021636 (c= -0.14709245)
139a -> 144a : 0.029537 (c= 0.17186373)
140a -> 141a : 0.493712 (c= -0.70264618)
140a -> 142a : 0.021983 (c= -0.14826775)
140a -> 144a : 0.030323 (c= 0.17413609)

STATE 2: E= 0.085954 au 2.339 eV 18864.8 cm**-1 = 0.000000
139a -> 141a : 0.493490 (c= 0.70248856)
139a -> 142a : 0.022278 (c= -0.14925782)
139a -> 144a : 0.027986 (c= 0.16728926)
140a -> 141a : 0.380403 (c= -0.61676836)
140a -> 142a : 0.021947 (c= 0.14814422)
140a -> 144a : 0.027699 (c= -0.16642982)

STATE 3: E= 0.132745 au 3.612 eV 29134.1 cm**-1 = 0.000000
139a -> 142a : 0.123433 (c= 0.35133024)
139a -> 143a : 0.221706 (c= -0.47085677)
139a -> 144a : 0.117215 (c= 0.34236621)
139a -> 146a : 0.039887 (c= -0.19971670)
140a -> 142a : 0.072587 (c= -0.26941893)
140a -> 143a : 0.269701 (c= 0.51932752)
140a -> 144a : 0.061824 (c= -0.24864433)
140a -> 146a : 0.039400 (c= 0.19849355)

STATE 4: E= 0.133335 au 3.628 eV 29263.6 cm**-1 = 0.000000
137a -> 145a : 0.011128 (c= 0.10548751)
139a -> 142a : 0.086160 (c= 0.29353050)
139a -> 143a : 0.212033 (c= 0.46047060)
139a -> 144a : 0.140644 (c= 0.37502547)
140a -> 142a : 0.142376 (c= 0.37732800)
140a -> 143a : 0.156057 (c= 0.39504032)
140a -> 144a : 0.211858 (c= 0.46028051)

When I try to calculate the transition probabilities, it doesn't give back 100%. The system is a closed shell. Any suggestion? or can it be done in Multiwfn? I tried to plot the Uv-vis spectra and see the transitions by this.
Multiwfn sp.out > 11 > 3 > 15 > 0 > 533.04910
What I get,
Sum of absolute values of all transitions: 41.19493
The individual terms are ranked by magnitude of contribution:
#Transition Contribution %
2 36.69845 89.085
1 4.34905 10.557
3 0.12731 0.309
7 0.01532 0.037
4 0.00242 0.006
8 0.00215 0.005
6 0.00015 0.000
5 0.00007 0.000
9 0.00000 0.000
10 0.00000 0.000

How does it calculate the transition percentage?

prasanta13 · Multiwfn and wavefunction analysis

Thank you Prof. Tian.

prasanta13 · Multiwfn and wavefunction analysis

Hi there,
I was wondering if there is a way to export MO cube files using Multiwfn.
We can visualize the HOMO, LUMO etc, but can we export the cube files?

prasanta13 · Multiwfn and wavefunction analysis

Okay, got it.
Thank You, Prof Tian.

prasanta13 · Multiwfn and wavefunction analysis

Hi Prof Tian,
For testing purposes, I have calculated a single-point (Hartree Fock) calculation on H2 molecule with ORCA and PSI4, followed by reading the .gbw and .fchk file by Multiwfn and exporting electron density to a .txt file with the high grid.
The steps I have taken are as follows.
Multwfn H2.gbw(or H2.fchk) > 5 > 1 > 3 >3

To integrate the electron density, I wrote a small python code which shows the total value of density as 0.28, which should be 2 (for H2). There can be some problems with my program, but when I cross-checked the data, I observed that the 4th column (density value) has only one maxima. Maxima value I obtained is 0.429159635 (from my program) and by using grep "4.291596" output.txt I got only one value "4.29159635E-001".

For H2 molecule, there should be two equal maximum values of density, right?

What could get wrong, any idea?

prasanta13 · Multiwfn and wavefunction analysis

Thank You Prof. Tian. It works, I am now analyzing the output.

prasanta13 · Multiwfn and wavefunction analysis

Yes
Main Menu > 5 > 1 > 3 > 3

prasanta13 · Multiwfn and wavefunction analysis

I am sorry for this misunderstanding Prof. Tian.
What I want to do, for example,
1. Take a molecule, suppose CH2Cl2 , calculate total density > export as 4 column txt file (done via multiwfn)
2. Now I want the density of CH2 and Cl2 separately and export density of CH2 and Cl2 as 4 column txt file.

Since Hirshfeld (or iterative) partitions works well for obtaining atomic densities from a molecule, in a similar fashion, can I get fragment densities as well?

Thank you Prof. Tian for your kind help.

prasanta13 · Multiwfn and wavefunction analysis

Hi Prof Tian,
I want to partition the total molecular density into small fragment densities based on Hirshfeld method. After that, I need those densities to be outputted as four column .txt file.
Can it be done in Multiwfn?

Thanks and Regards,
Prasanta

prasanta13 · Multiwfn and wavefunction analysis

Dear Developers,

1. In many of the analysis, such as ESP, NCI etc etc, we go deeper into the Multiwfn submenu and can't view the molecule. Some time it becomes necessary to view the molecule the in the same way as Main Menu > 0. Can this be allowed?

2. If by any means, the x, y, z- axis can be shown with the e Density or ESP contour or in a similar types of plots.

prasanta13 · Multiwfn and wavefunction analysis

Many many thanks.

prasanta13 · Multiwfn and wavefunction analysis

Prof Tian, I have used three points to define the plane. I took the liberty to select three points to define such a plane that gives me the maximum atoms to be shown.

By the way, Can this plot be extracted to a script like matplotlib or gnuplot such that one can tweek through the setting?

prasanta13 · Multiwfn and wavefunction analysis

Hi there, I tried to plot the ESP contour diagram of a molecule. It is not fitted inside the default print area. Let me show by this image.

Are there an method by which I can fit the image inside the rectangle? Or can I increase the size of the rectangle?

prasanta13 · Multiwfn and wavefunction analysis

Dear Users and Prof Tian,
For non-covalent interactions (especially the halogen bonding), the sigma-hole is the LEwis acid region, which can also be observed from the Fukui function for nucleophilic attack (f+). Its condensed to atom variant (fk+) can also be calculated from Multiwfn. However, is it possible to calculated the fk+ for the pi-holes or delta-holes?

prasanta13 · Multiwfn and wavefunction analysis

Dear Tian, I am also facing same problem. I was using the 3.7 dev version and changed to stable one but the problem persists when using the .gbw file (since the wfn file do not contain the basis information, as stated by Multiwfn).
The error is as followed, when utilizing "4.2.4 Decompose properties at a critical point as orbital contributions" on the manual.

Calculating atomic contributions to orbitals by Hirshfeld method...
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred
forrtl: severe (174): SIGSEGV, segmentation fault occurred

I am using Ubuntu 18.04
The bash section is as followed
#Multiwfn
export KMP_STACKSIZE=20000000000
export Multiwfnpath=/home/prasanta/Multiwfn/Multiwfn_3.7_bin_Linux/
export PATH=$PATH:/home/prasanta/Multiwfn/Multiwfn_3.7_bin_Linux/
ulimit -s unlimited

It also sourced properly.
What could be the problem?
Thanks in advance...

prasanta13 · Multiwfn and wavefunction analysis

Thank you Tian, I will try and get back to you.

prasanta13 · Multiwfn and wavefunction analysis

Dear Prof Tian,

I have encountered a problem in EDD. I have optimized a NCI complex using m062x/def2tzvpp in ORCA. The .wfn files are formed.
1. In the 4.5.5 section, you have mentioned to use NOSYMM keyword for gaussian, does the similar happens with ORCA?
2. One of my monomer is open-shell, so I used UM062X, other one is closed-shell and the complex is thus treated in UKS. The EDD using UKS shows abrupt results, should I treat the system as ROKS or UKS?

Thank you

prasanta13 · Multiwfn and wavefunction analysis

Dear Prof Tian Lu and/or other members
I am trying to investigate the Non-Covalent interaction between radical (CH3) and halogen bond donors. I find three very close/dense NCI isosurfaces which are red/blue (weak v d w interaction), so i started to use AIM to search for 3,-1 bcps. The BCPs do not reflect the proper interaction sites as observed from the NCI analysis.
Out of the three NCI surfaces, I find two 3,-1 bcp and one 3,+1 rcp. I do not know if the RCP is attractive or repulsive contribution. The bond path is also wrong. The poincare-hopf relationship also do not hold.
what to do?

prasanta13 · Multiwfn and wavefunction analysis

Hello Dr Tian Lu
I am posting few issues relating to the generation of Vsmax.
I have optimized few molecules with RI-MP2/aug-cc-pvtz in ORCA 4.2.1 and generated .wfn and .wfx files. I loaded those files with Multiwfn and went to option 12 to 12 (Quantitative analysis of Molecular surface) and start analysis. I have Gaussian configured with Multiwfn but the Multiwfn generates the surface in its own engine. The results obtained are ridiculous. The reported Vs,max of the same region of the same molecule (F2) is 14, whereas Multiwfn shows it 53 kcal/mol.
So, where the problem is?
a. The ORCA wfn files can not be used?
b. Only the gaussian fchk files to be used?
c. The cubegen can work with only fchk files but not of wfn/wfx files?
d. What is the cause of this error in Vsmax value.

Thanking You.

prasanta13 · Multiwfn and wavefunction analysis

Hi there, I am currently studying the difference in electronic structure of carbenes. Suppose, there are three species, singlet and triplet CH2, and CH3 radical. How can I distinguish the location of the valence shell electron of these species?

prasanta13 · Multiwfn and wavefunction analysis

Prof Lu,
I am trying to model the electron transfer from superoxide radical to benzoquinone molecule in the ground state. Can it be done with CDA approach? Or there are other better approaches?

prasanta13 · Multiwfn and wavefunction analysis

One more small question. It does analyze the CDFT parameters using Hirshfeld charges. As these parameters are very much dependent upon atomic charge, DFT methods and basis sets, I just ask, Can I use mulliken and ChelPG or natural charge to calculate them? Can I use cam-b3lyp, m062x and wb97xd method and aug-cc-pvtz basis set?

prasanta13 · Multiwfn and wavefunction analysis

Thank You Sir, I was testing this for CH4 molecule, and it worked fine with 6-311++G**, with 0 1 for N electron state. However, when it stops functioning with OH radical. Let me detail the procedure.
I load OH.fchk > 100 > 16 > 1
I input ub3lyp/6-311++G**
I input 0 2
Program hangs, it do not output the wfn files it did for previous time.

Thanks in Advance

Multiwfn forum

#1Re:Quantum Chemistry»Calculate the one-particle and two-particle density matrix»2023-10-09 11:44:08

#2Re:Quantum Chemistry»Calculate the one-particle and two-particle density matrix»2023-08-11 12:54:46

#3Quantum Chemistry»Calculate the one-particle and two-particle density matrix»2023-08-09 12:07:22

#4Re:Multiwfn and wavefunction analysis»Export MO cube file from gbw or fch file»2022-08-22 05:31:55

#5Re:Multiwfn and wavefunction analysis»Export MO cube file from gbw or fch file»2022-08-21 13:21:35

#6Re:Multiwfn and wavefunction analysis»TD-DFT transition probabilities from ORCA output»2022-08-16 06:22:05

#7Re:Multiwfn and wavefunction analysis»TD-DFT transition probabilities from ORCA output»2022-08-13 05:13:59

#8Multiwfn and wavefunction analysis»TD-DFT transition probabilities from ORCA output»2022-08-12 07:33:11

#9Re:Multiwfn and wavefunction analysis»Export MO cube file from gbw or fch file»2022-08-12 07:24:54

#10Multiwfn and wavefunction analysis»Export MO cube file from gbw or fch file»2022-08-11 06:28:51

#11Re:Multiwfn and wavefunction analysis»Electron density xyz-type output problem»2022-07-05 04:21:25

#12Multiwfn and wavefunction analysis»Electron density xyz-type output problem»2022-07-04 11:21:01

#13Re:Multiwfn and wavefunction analysis»Hirshfeld partition of molecular density»2022-06-17 14:00:30

#14Re:Multiwfn and wavefunction analysis»Hirshfeld partition of molecular density»2022-06-10 10:32:12

#15Re:Multiwfn and wavefunction analysis»Hirshfeld partition of molecular density»2022-06-10 06:18:36

#16Multiwfn and wavefunction analysis»Hirshfeld partition of molecular density»2022-06-09 06:32:12

#17Multiwfn and wavefunction analysis»Multiple Feature Request»2021-09-08 04:44:59

#18Re:Multiwfn and wavefunction analysis»ETS-NOCV has been supported in Multiwfn!»2021-09-07 06:32:51

#19Re:Multiwfn and wavefunction analysis»ESP Plot not covered fully inside the area»2021-09-07 06:28:03

#20Multiwfn and wavefunction analysis»ESP Plot not covered fully inside the area»2021-09-03 10:42:14

#21Multiwfn and wavefunction analysis»Condensed to atom Fukui Function for pi-holes»2020-11-22 04:58:00

#22Re:Multiwfn and wavefunction analysis»error forrtl: severe (174): SIGSEGV, segmentation fault»2020-09-06 13:26:15

#23Re:Multiwfn and wavefunction analysis»Electron Density Difference Plot with Multiwfn»2020-09-05 14:18:33

#24Re:Multiwfn and wavefunction analysis»Electron Density Difference Plot with Multiwfn»2020-09-05 07:08:20

#25Multiwfn and wavefunction analysis»AIM analysis»2020-08-28 06:49:57

#26Multiwfn and wavefunction analysis»ESP generation»2020-05-21 06:27:38

#27Multiwfn and wavefunction analysis»Localization of Electron»2020-01-15 13:27:24

#28Re:Multiwfn and wavefunction analysis»On the calculation of charge transfer between donor and acceptor»2020-01-09 13:57:50

#29Re:Multiwfn and wavefunction analysis»Analysis of Fukui function»2019-07-31 06:47:20

#30Re:Multiwfn and wavefunction analysis»Analysis of Fukui function»2019-07-31 06:34:19

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