From owner-chemistry@ccl.net Wed Oct 30 01:43:00 2024 From: "Grigoriy Zhurko reg_zhurko=-=chemcraftprog.com" To: CCL Subject: CCL:G: Printing the Hessian in Orca output files Message-Id: <-55236-241030013907-22322-TTv3DcpCgZwBb8M8qdVVzQ,,server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 30 Oct 2024 08:38:56 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko.:.chemcraftprog.com] > I am implementing the computation of vibrational frequencies in RRHO approximation in my program (this can be useful for quick computation of the kinetic isotope effects). My program can read a Gaussian .fch file with the Hessian, and compute the frequencies. My question is, how can I enable the printout of the Hessian in Orca output files, and also in the output files produced by other QC packages (Gamess, Molpro, NWChem, etc). > Maybe somebody can send here some samples of Gamess/Molpro files with a hessian and frequencies, and I will implement the frequencies computation and verify it with these files. I am sorry if my question was noob, now I found that with Orca the Hessian is printed in the .hess file. However for other packages (Gamess, Molpro, Dalton, NWChem, CFour, Priroda) I can't run the jobs myself, so I will be glad if somebody sends to me some samples of output files which contain the Hessian. Besides that, I found some difference between the frequencies computed by my program and Orca, as if the Orca used other atomic masses. And still a very interesting question for me is whether the Hessian can be restored from the frequencies and normal modes, if the lower 6 frequencies (translational/rotational) are not printed in the file. Grigoriy Zhurko https://chemcraftprog.com From owner-chemistry@ccl.net Wed Oct 30 03:39:00 2024 From: "Frank Jensen frj:_:chem.au.dk" To: CCL Subject: CCL:G: SV: CCL:G: Printing the Hessian in Orca output files Message-Id: <-55237-241030033747-22688-wZCSe3q/bcSLCb0MMsUDxQ_+_server.ccl.net> X-Original-From: Frank Jensen Content-Language: da-DK Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 30 Oct 2024 07:37:36 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj..chem.au.dk] The 6 T + R modes can be constructed from the atomic positions and masses, this is how they are projected out of the Hessian in many programs. But since they should have 0 'frequencies' they can be added in any combination to the Cartesian Hessian, without affecting the vibrational degrees of freedom. In actual calculations, however, they are not exactly zero due to incomplete optimization and numerical noise, and unless you know what these residual frequencies are, you cannot exactly reproduce the original Cartesian Hessian. In the forward direction, you need a unitary transformation of the mass-weighted Hessian to bring it to diagonal form. The eigenvectors are the vibrational normal modes, and the eigenvalues are the frequencies, except for a scale factor, and it should thus be possible to reconstruct the unitary matrix, and use this for rotating back to the original Hessian. Regarding the masses, the common approach is to use the atomic (not nuclear) masses for the most common isotope, and not the mass calculated as the isotopic average (molar mass), perhaps this is where your difference is (?). And the use of atomic masses includes the mass of Z electrons, and thus assumes that exactly Z electrons move instantly with the nucleus in a molecule. This is slightly dodgy and leads to ambiguities in the calculated frequencies at the 0.x cm-1 level. Frank Frank Jensen Assoc. Prof. Department of Chemistry Aarhus University https://tildeweb.au.dk/au23758/ https://pure.au.dk/portal/en/frj..chem.au.dk -----Oprindelig meddelelse----- Fra: owner-chemistry+frj==chem.au.dk..ccl.net På vegne af Grigoriy Zhurko reg_zhurko=-=chemcraftprog.com Sendt: 30. oktober 2024 06:39 Til: Frank Jensen Emne: CCL:G: Printing the Hessian in Orca output files Sent to CCL by: Grigoriy Zhurko [reg_zhurko.:.chemcraftprog.com] > I am implementing the computation of vibrational frequencies in RRHO approximation in my program (this can be useful for quick computation of the kinetic isotope effects). My program can read a Gaussian .fch file with the Hessian, and compute the frequencies. My question is, how can I enable the printout of the Hessian in Orca output files, and also in the output files produced by other QC packages (Gamess, Molpro, NWChem, etc). > Maybe somebody can send here some samples of Gamess/Molpro files with a hessian and frequencies, and I will implement the frequencies computation and verify it with these files. I am sorry if my question was noob, now I found that with Orca the Hessian is printed in the .hess file. However for other packages (Gamess, Molpro, Dalton, NWChem, CFour, Priroda) I can't run the jobs myself, so I will be glad if somebody sends to me some samples of output files which contain the Hessian. Besides that, I found some difference between the frequencies computed by my program and Orca, as if the Orca used other atomic masses. And still a very interesting question for me is whether the Hessian can be restored from the frequencies and normal modes, if the lower 6 frequencies (translational/rotational) are not printed in the file. Grigoriy Zhurko https://chemcraftprog.com/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml/http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Oct 30 04:14:00 2024 From: "Kjell Jorner kjell.jorner _ gmail.com" To: CCL Subject: CCL:G: Printing the Hessian in Orca output files Message-Id: <-55238-241030040659-1033-2Dd60tiueh6OGtTv/TBOtA,+,server.ccl.net> X-Original-From: Kjell Jorner Content-Type: multipart/alternative; boundary="Apple-Mail=_6B8B8BA7-FBEC-4FC8-896D-1C333FD61A74" Date: Wed, 30 Oct 2024 09:06:42 +0100 Mime-Version: 1.0 (Mac OS X Mail 16.0 \(3826.200.121\)) Sent to CCL by: Kjell Jorner [kjell.jorner:_:gmail.com] --Apple-Mail=_6B8B8BA7-FBEC-4FC8-896D-1C333FD61A74 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Grigoriy, Without answering your specific question, you might want to check out = the UniMoVib program from Wenli Zoo: https://github.com/zorkzou/UniMoVib It would at least be interesting for you in terms of comparing to the = results of your own program. Best regards, Kjell Jorner > On 30 Oct 2024, at 06:38, Grigoriy Zhurko = reg_zhurko=3D-=3Dchemcraftprog.com wrote: >=20 >=20 > Sent to CCL by: Grigoriy Zhurko [reg_zhurko.:.chemcraftprog.com] >> I am implementing the computation of vibrational frequencies in RRHO = approximation in my program (this can be useful for quick computation of = the kinetic isotope effects). My program can read a Gaussian .fch file = with the Hessian, and compute the frequencies. My question is, how can I = enable the printout of the Hessian in Orca output files, and also in the = output files produced by other QC packages (Gamess, Molpro, NWChem, = etc). >=20 >> Maybe somebody can send here some samples of Gamess/Molpro files with = a hessian and frequencies, and I will implement the frequencies = computation and verify it with these files. >=20 > I am sorry if my question was noob, now I found that with Orca the = Hessian is printed in the .hess file. However for other packages = (Gamess, Molpro, Dalton, NWChem, CFour, Priroda) I can't run the jobs = myself, so I will be glad if somebody sends to me some samples of output = files which contain the Hessian. Besides that, I found some difference = between the frequencies computed by my program and Orca, as if the Orca = used other atomic masses. And still a very interesting question for me = is whether the Hessian can be restored from the frequencies and normal = modes, if the lower 6 frequencies (translational/rotational) are not = printed in the file. >=20 > Grigoriy Zhurko > https://chemcraftprog.com >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_6B8B8BA7-FBEC-4FC8-896D-1C333FD61A74 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = Grigoriy,

Without answering your specific = question, you might want to check out the UniMoVib program from Wenli = Zoo: https://github.com/zorkzou/Un= iMoVib

It would at least be interesting for = you in terms of comparing to the results of your own = program.

Best regards,
Kjell = Jorner


On 30 Oct 2024, at 06:38, Grigoriy Zhurko = reg_zhurko=3D-=3Dchemcraftprog.com <owner-chemistry~~ccl.net> = wrote:


Sent = to CCL by: Grigoriy Zhurko = [reg_zhurko.:.chemcraftprog.com]
I am = implementing the computation of vibrational frequencies in RRHO = approximation in my program (this can be useful for quick computation of = the kinetic isotope effects). My program can read a Gaussian .fch file = with the Hessian, and compute the frequencies. My question is, how can I = enable the printout of the Hessian in Orca output files, and also in the = output files produced by other QC packages (Gamess, Molpro, NWChem, = etc).

Maybe somebody can = send here some samples of Gamess/Molpro files with a hessian and = frequencies, and I will implement the frequencies computation and verify = it with these files.

I am sorry if my question was = noob, now I found that with Orca the Hessian is printed in the .hess = file. However for other packages (Gamess, Molpro, Dalton, NWChem, CFour, = Priroda) I can't run the jobs myself, so I will be glad if somebody = sends to me some samples of output files which contain the Hessian. = Besides that, I found some difference between the frequencies computed = by my program and Orca, as if the Orca used other atomic masses. And = still a very interesting question for me is whether the Hessian can be = restored from the frequencies and normal modes, if the lower 6 = frequencies (translational/rotational) are not printed in the = file.

Grigoriy = Zhurko
https://chemcraftprog.com



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fSIgc3R5bGU9IkZPTlQtU0laRTogOHB0Ij48Zm9udCBmYWNlPSJBcmlhbCI+PC9mb250Pjxmb250 IHNpemU9IiswIj48L2ZvbnQ+PC9wPg0KPHAgY2xhc3M9IntJbXByaW50LlVuaXF1ZUlEfSIgc3R5 bGU9IkZPTlQtU0laRTogOHB0Ij48Zm9udCBmYWNlPSJBcmlhbCI+PC9mb250PjwvcD4NCjxwIGNs YXNzPSJ7SW1wcmludC5VbmlxdWVJRH0iIHN0eWxlPSJGT05ULVNJWkU6IDhwdCI+PC9wPg0KPHAg Y2xhc3M9IntJbXByaW50LlVuaXF1ZUlEfSIgc3R5bGU9IkZPTlQtU0laRTogOHB0Ij48L3A+DQo8 L2JvZHk+DQo8L2h0bWw+DQo= --_000_379C51FB4EFB43E480F949FDF97742E1astrazenecacom_-- From owner-chemistry@ccl.net Wed Oct 30 09:04:01 2024 From: "Grigoriy Zhurko reg_zhurko[A]chemcraftprog.com" To: CCL Subject: CCL:G: Printing the Hessian in Orca output files Message-Id: <-55240-241030085804-32155-ipVMGbFX4vMpM1EbNDTfWQ*_*server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 30 Oct 2024 15:57:53 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko**chemcraftprog.com] > There are two different ways of calculating frequencies. The straight calculation gives non-zero values for the six lowest modes (arguably incorrect). Some programs first project the Hessian to make the eigenvalues for translation and rotation (the six lowest modes) exactly equal to zero. This shifts the remaining eigenvalues (and thus frequencies) by a small amount. Maybe all QC packages perform this low-freqs elimination? In the Gaussian output for toluene, I see: Low frequencies --- -4.9925 0.0001 0.0005 0.0008 10.0345 19.9870 Low frequencies --- 27.9813 208.8178 343.5002 Then, in the table of vibrational modes in this file, the first freq is 27.3674. When I computed the freqs with my program, I got the value 27.9813. So it seems that Gaussian performs this elimination. I have a question, how these T+R frequencies are, firstly, identified (in particular when the vibrational frequencies contain negative ones), and secondly, eliminated (how the final vibrational frequencies are computed). I try to understand the mathematical theory of this; possibly, if we have a N*N Hessian, this means that we have N vectors in N-dimensional space, and performing the matrix diagonalization, we rotate these N vectors with some N*N rotational matrix so that the Hessian becomes diagonal. Then, since the matrix diagonalization does not fully eliminate the T+R freqs, we perform some more rotation of these N vectors after that, and so the T+R vectors become exactly zero. Am I correct? When I’ll implement this feature in Chemcraft, its users will be able to open a file with frequencies and quickly recalculate the frequencies with other isotopes, for estimating the isotopic substitution effects on the spectra or kinetics. And here I have one more question. As far as I understand, using the averaged atomic masses is not fully correct, since the real compounds are mixtures of molecules with random isotopic compositions; and possibly I should also implement a long computation of a spectrum of a mixture of molecules with random isotopes (similarly to the computation of mass spectra, where e.g. C ion produces two peaks on 12.0 and 13.003 DA, C2 ion produces three peaks on 24.0, 25.003 and 26.007 DA, etc)? Grigoriy Zhurko https://chemcraftprog.com From owner-chemistry@ccl.net Wed Oct 30 10:42:00 2024 From: "=?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= mariusz.radon+/-uj.edu.pl" To: CCL Subject: CCL:G: Printing the Hessian in Orca output files Message-Id: <-55241-241030104023-30917-xX9d02LYkOmlbs7AsHosUw#server.ccl.net> X-Original-From: =?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= Content-ID: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Wed, 30 Oct 2024 14:40:11 +0000 MIME-Version: 1.0 Sent to CCL by: =?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= [mariusz.radon[]uj.edu.pl] Dear Grigoriy: > On 30 Oct 2024, at 13:57, Grigoriy Zhurko reg_zhurko[A]chemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko**chemcraftprog.com] >> There are two different ways of calculating frequencies. The straight calculation gives non-zero values for the six lowest modes (arguably incorrect). Some programs first project the Hessian to make the eigenvalues for translation and rotation (the six lowest modes) exactly equal to zero. This shifts the remaining eigenvalues (and thus frequencies) by a small amount. > > Maybe all QC packages perform this low-freqs elimination? In the Gaussian output for toluene, I see: > > Low frequencies --- -4.9925 0.0001 0.0005 0.0008 10.0345 19.9870 > Low frequencies --- 27.9813 208.8178 343.5002 > > Then, in the table of vibrational modes in this file, the first freq is 27.3674. When I computed the freqs with my program, I got the value 27.9813. So it seems that Gaussian performs this elimination. Yes, it does. You can read more about the procedures used in Gaussian in their whitepaper on vibrational analysis https://gaussian.com/vib/ This may also address some of your questions below. And I guess that many other programs use similar procedures as Gaussian. Best wishes, Mariusz > I have a question, how these T+R frequencies are, firstly, identified (in particular when the vibrational frequencies contain negative ones), and secondly, eliminated (how the final vibrational frequencies are computed). > I try to understand the mathematical theory of this; possibly, if we have a N*N Hessian, this means that we have N vectors in N-dimensional space, and performing the matrix diagonalization, we rotate these N vectors with some N*N rotational matrix so that the Hessian becomes diagonal. Then, since the matrix diagonalization does not fully eliminate the T+R freqs, we perform some more rotation of these N vectors after that, and so the T+R vectors become exactly zero. Am I correct? > When I’ll implement this feature in Chemcraft, its users will be able to open a file with frequencies and quickly recalculate the frequencies with other isotopes, for estimating the isotopic substitution effects on the spectra or kinetics. And here I have one more question. As far as I understand, using the averaged atomic masses is not fully correct, since the real compounds are mixtures of molecules with random isotopic compositions; and possibly I should also implement a long computation of a spectrum of a mixture of molecules with random isotopes (similarly to the computation of mass spectra, where e.g. C ion produces two peaks on 12.0 and 13.003 DA, C2 ion produces three peaks on 24.0, 25.003 and 26.007 DA, etc)? > > Grigoriy Zhurko > https://chemcraftprog.com -- Mariusz Radon, Ph.D., D.Sc. Associate Professor Faculty of Chemistry, Jagiellonian University Address: Gronostajowa 2, 30-387 Krakow, Poland Room C1-06, Phone: 48-12-686-24-89 E-mail: mradon .. chemia.uj.edu.pl (mariusz.radon .. uj.edu.pl) Web: https://tungsten.ch.uj.edu.pl/~mradon ORCID: https://orcid.org/0000-0002-1901-8521 From owner-chemistry@ccl.net Wed Oct 30 11:47:00 2024 From: "Norrby, Per-Ola Per-Ola.Norrby]=[astrazeneca.com" To: CCL Subject: CCL: Printing the Hessian in Orca output files Message-Id: <-55242-241030114215-11543-DMRhehuD5J41tA861Usb5Q(!)server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DB9PR04MB844599E22DB2516B9A0BA7F3CA542DB9PR04MB8445eurp_" Date: Wed, 30 Oct 2024 15:41:59 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby^astrazeneca.com] --_000_DB9PR04MB844599E22DB2516B9A0BA7F3CA542DB9PR04MB8445eurp_ Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 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most abundant natural isotope. Cory -----Original Message----- > From: owner-chemistry+cory.pye==smu.ca]_[ccl.net On Behalf Of Grigoriy Zhurko reg_zhurko[A]chemcraftprog.com Sent: October 30, 2024 9:58 AM To: Cory Pye Subject: CCL:G: Printing the Hessian in Orca output files Sent to CCL by: Grigoriy Zhurko [reg_zhurko**chemcraftprog.com] > There are two different ways of calculating frequencies. The straight calculation gives non-zero values for the six lowest modes (arguably incorrect). Some programs first project the Hessian to make the eigenvalues for translation and rotation (the six lowest modes) exactly equal to zero. This shifts the remaining eigenvalues (and thus frequencies) by a small amount. Maybe all QC packages perform this low-freqs elimination? In the Gaussian output for toluene, I see: Low frequencies --- -4.9925 0.0001 0.0005 0.0008 10.0345 19.9870 Low frequencies --- 27.9813 208.8178 343.5002 Then, in the table of vibrational modes in this file, the first freq is 27.3674. When I computed the freqs with my program, I got the value 27.9813. So it seems that Gaussian performs this elimination. I have a question, how these T+R frequencies are, firstly, identified (in particular when the vibrational frequencies contain negative ones), and secondly, eliminated (how the final vibrational frequencies are computed). I try to understand the mathematical theory of this; possibly, if we have a N*N Hessian, this means that we have N vectors in N-dimensional space, and performing the matrix diagonalization, we rotate these N vectors with some N*N rotational matrix so that the Hessian becomes diagonal. Then, since the matrix diagonalization does not fully eliminate the T+R freqs, we perform some more rotation of these N vectors after that, and so the T+R vectors become exactly zero. Am I correct? When I'll implement this feature in Chemcraft, its users will be able to open a file with frequencies and quickly recalculate the frequencies with other isotopes, for estimating the isotopic substitution effects on the spectra or kinetics. And here I have one more question. As far as I understand, using the averaged atomic masses is not fully correct, since the real compounds are mixtures of molecules with random isotopic compositions; and possibly I should also implement a long computation of a spectrum of a mixture of molecules with random isotopes (similarly to the computation of mass spectra, where e.g. C ion produces two peaks on 12.0 and 13.003 DA, C2 ion produces three peaks on 24.0, 25.003 and 26.007 DA, etc)? Grigoriy Zhurko https://chemcraftprog.com/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml/http://www.ccl.net/spammers.txt