From owner-chemistry "-at-" ccl.net Wed Dec 20 11:02:01 2017 From: "Martin C. Schwarzer schwarzer{}mail.de" To: CCL Subject: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian Message-Id: <-53105-171220092558-1339-sYNBaA8zkwwaJPbJWW3D1Q.:.server.ccl.net> X-Original-From: "Martin C. Schwarzer" Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="mPdF7zPSIvA7BqMnD6Yg4lm0mTqHxyetK" Date: Wed, 20 Dec 2017 23:25:26 +0900 MIME-Version: 1.0 Sent to CCL by: "Martin C. Schwarzer" [schwarzer!=!mail.de] This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --mPdF7zPSIvA7BqMnD6Yg4lm0mTqHxyetK Content-Type: multipart/mixed; boundary="vPffwgl2nPThZBpjtpfDUhhd3LmwBGFA4"; protected-headers="v1" > From: "Martin C. Schwarzer" To: CCL Subscribers Message-ID: <48044a4e-fbbf-b873-e10a-99229ead509d#mail.de> Subject: Re: CCL:G: Combining Z-matrix with Cartesian coordinates in Gaussian References: <53097-171219105507-3259-ECRg4LaDg3cm/SIQOwak0A#server.ccl.net> In-Reply-To: <53097-171219105507-3259-ECRg4LaDg3cm/SIQOwak0A#server.ccl.net> --vPffwgl2nPThZBpjtpfDUhhd3LmwBGFA4 Content-Type: text/plain; charset=utf-8 Content-Language: de-DE Content-Transfer-Encoding: quoted-printable Hello, In Gaussian, unfortunately a relaxed scan can only be done via OPT(ModRedundant), which also means that you cannot use dummy atoms. See the following Q&A for more information: https://chemistry.stackexchange.com/q/49483/4945 You can still perform a rigid scan, but that has to be done via a (symbolic) z-matrix, invoked via the SCAN keyword. E.g.: https://chemistry.stackexchange.com/q/54022/4945 An example for performing a rigid scan with a mixed style coordinates can be found here: https://chemistry.stackexchange.com/q/62886/4945 The z-matrix in your input is, as others pointed out, half frozen. Only the variables in the "Variables" section will actually be optimised, and it will be optimised, not scanned. I am not sure whether the "Constants" section will be treated as constant, because that should require the POPT keyword. E.g.: https://chemistry.stackexchange.com/q/39057/4945 If I understand correctly, you would like to scan the out-of-plane displacement of zinc. The closest to a relaxed scan you can (probably) get is to manually prepare multiple coordinate files where you move the zinc along the z-axis, and freeze all the Zn-N distances with OPT(ModRedundant). Best regards, Martin Am Wed 20/12/2017 um 12:55 AM schrieb Demian Riccardi demianriccardi:gmail.com: > Is it really a valid geometry?=C2=A0 From a quick glance at your coordi= nates, > it appears that all your Z-matrix coordinates are defined, first, > relative to the dummy atom and then all the absolute coordinates come > next. Is it obvious how the two pieces would fit together?=C2=A0 You sh= ould > make sure your coordinates make sense with what Gaussian expects. >=20 > http://gaussian.com/zmat/ >=20 >=20 > On Tue, Dec 19, 2017 at 6:20 AM, Guzman, Francisco fg58%njit.edu > > wrote: >=20 > What are the errors? It's also unclear what you are trying to do. > Are you trying to do a relaxed scan (PES), rigid scan,=C2=A0 or jus= t > optimize? If it's a relaxed scan, then opt=3Dmodredundant is > required.=C2=A0 I believe for any modredundant job Gaussian interna= lly > optimizes with a z-matrix only. Something along the lines of forcin= g > the job to optimize using cartesian coordinates, opt=3D(modredudant= , > cartersian), will not work. For a rigid scan (molecule is frozen > except bond/angle/dihedral of interest) use the "scan" keyword > followed by specifying in the z-matrix which angle/bond/dihedral of= > interest is to be scanned. Scan also requires the use of a z-matrix= =2E >=20 > I've had many many issues with linear angles myself.=C2=A0 If it's = just > an optimization, inserting a dummy atom works just fine. However, > for a PES it seems to me that the dummy atom is only considered in > the first step of your scan and is subsequently discarded. Hence, i= f > a linear angle appears at any place during the scan, my calculation= s > tend to terminate with something along the lines of error L9999, > "Error linear angle in bend".=C2=A0 >=20 > Maybe try another program if this is an issue. NWCHEM could work. >=20 > On Mon, Dec 18, 2017 at 9:34 AM, Grigoriy Zhurko > reg_zhurko||chemcraftprog.com > > > wrote: >=20 >=20 > Sent to CCL by: Grigoriy Zhurko [reg_zhurko]~[chemcraftprog.com= > ] > Hello, >=20 > I need to perform a PES scan in Gaussian, so that the distance > between an atom and the center between two other atoms will be > scanned. > When I need to simply scan an iteratomic distance, I use > OPT(MODREDUNDANT). But in current case I have to use a z-matrix= > and add a dummy atom (the center between two real atoms). > It is possible to use only Z-matrix for this job, but the resul= t > becomes rather bad: the optimization starts with evident bugs > (probably because this geometry has rings). > I tried to combine the Z-matrix with the Cartesians. I created > the following input file: >=20 > %NPROCSHARED=3D3 > =C2=A0#P uwB97XD/6-31G(D,P) OPT(Z-Matrix,LOOSE) > =C2=A0NOSYMM >=20 > =C2=A0Silicon >=20 > =C2=A00 1 > =C2=A0X > =C2=A0N 1 R12 > =C2=A0X 1 1.400000 2 90.000000 > =C2=A0N 1 R12 3 90.000000 2 180.000000 > =C2=A0N 1 R15 2 A215 3 -90.000000 > =C2=A0N 1 R16 3 A316 5 D5316 > =C2=A0Zn 1 R17 2 A217 5 -D5217 > =C2=A06 0.000000000 2.863016000 1.101006000 > =C2=A06 0.000000000 2.425840000 2.425840000 > =C2=A06 0.000000000 1.101006000 2.863016000 > =C2=A01 0.000000000 3.193595000 3.193595000 > =C2=A06 0.000000000 2.863016000 -1.101006000 > =C2=A06 0.000000000 2.425840000 -2.425840000 > =C2=A06 0.000000000 1.101006000 -2.863016000 > =C2=A01 0.000000000 3.193595000 -3.193595000 > =C2=A06 0.000000000 -1.101006000 -2.863016000 > =C2=A06 0.000000000 -2.425840000 -2.425840000 > =C2=A06 0.000000000 -2.863016000 -1.101006000 > =C2=A01 0.000000000 -3.193595000 -3.193595000 > =C2=A06 0.000000000 -2.863016000 1.101006000 > =C2=A06 0.000000000 -2.425840000 2.425840000 > =C2=A06 0.000000000 -1.101006000 2.863016000 > =C2=A01 0.000000000 -3.193595000 3.193595000 > =C2=A06 0.000000000 -4.245855000 0.681548000 > =C2=A06 0.000000000 -4.245855000 -0.681548000 > =C2=A06 0.000000000 -0.681548000 -4.245855000 > =C2=A06 0.000000000 0.681548000 -4.245855000 > =C2=A06 0.000000000 -0.681548000 4.245855000 > =C2=A06 0.000000000 0.681548000 4.245855000 > =C2=A06 0.000000000 4.245855000 0.681548000 > =C2=A06 0.000000000 4.245855000 -0.681548000 > =C2=A01 0.000000000 -5.096481000 1.350466000 > =C2=A01 0.000000000 -5.096481000 -1.350466000 > =C2=A01 0.000000000 -1.350466000 -5.096481000 > =C2=A01 0.000000000 1.350466000 -5.096481000 > =C2=A01 0.000000000 5.096481000 -1.350466000 > =C2=A01 0.000000000 5.096481000 1.350466000 > =C2=A01 0.000000000 -1.350466000 5.096481000 > =C2=A01 0.000000000 1.350466000 5.096481000 > =C2=A0Variables: > =C2=A0R12 =3D 2.04198300 > =C2=A0R15 =3D 2.04198300 > =C2=A0A215 =3D 90.00000000 > =C2=A0R16 =3D 2.04198300 > =C2=A0A316 =3D 90.00000000 > =C2=A0D5316 =3D 180.00000000 > =C2=A0A217 =3D 90.00000000 > =C2=A0D5217 =3D 90.00000000 > =C2=A0constants > =C2=A0R17 =3D 0.40000000 s 20 0.2 >=20 > This job constructs a valid geometry, the optimization starts, > but it starts incorrectly: during the optimization, only the > Z-matrix parameters are varied, while the coordinates of most > atoms are fixed. Can I do something to make Gaussian optimize > these atomic coordinates as well? >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing= > script =3D-__ > E-mail to subscribers: CHEMISTRY|a|ccl.net > or use: > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage > >=20 > E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net > or use > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage > >=20> =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.sht= ml > >=20>=20> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > >=20 > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml > > __ =C2=A0 =C2=A0 =C2=A0> >=20> >=20 >=20 >=20 >=20 >=20 > --=20 > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email:=C2=A0fg58|a|njit.edu > ,=C2=A0guzman.research|a|gmail.com > >=20 >=20 --vPffwgl2nPThZBpjtpfDUhhd3LmwBGFA4-- --mPdF7zPSIvA7BqMnD6Yg4lm0mTqHxyetK Content-Type: application/pgp-signature; name="signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJaOnLlAAoJEIYALUULs51Wl90H/RsNK87Z4hPAQpejrGH/0ifF 6Y9djX1Dqxhus1uFzFLoBIOu3qGsBtRh+zt8Z5nSJmn9dkclE7V1LqxEnwAws8+n DWyCQv88GO11xFoKdN2Ha1NbrTtJ0sQCyfeC88HNMYCH9iQjiesRcrj51eCpupyG ZPacp6vVBfW3L73d22uOcxKION1HMyk+oUCca9TxGB0ezoVIk5JdHaALYHUTam+g UBGXlu+Q0z+nRYztmP1gwztiMf0i3I1JYBbb0bbZoqGlNOPGDvWbyLtqFRJTFB8N q3VdoeRWNmCugWEX4eVNZqo5tNlSz9KV9vhIbUanVBaed21tH325pqXLwY+bj00= =Dzma -----END PGP SIGNATURE----- --mPdF7zPSIvA7BqMnD6Yg4lm0mTqHxyetK--