From owner-chemistry@ccl.net Sun Oct 21 03:39:00 2018 From: "Andre Schleife schleife[]illinois.edu" To: CCL Subject: CCL: APS March Meeting 2018, Focus Topic 16.1.4 Message-Id: <-53515-181020222811-19475-JAbZIIyVutLQVf99X7fk9A{=}server.ccl.net> X-Original-From: "Andre Schleife" Date: Sat, 20 Oct 2018 22:28:08 -0400 Sent to CCL by: "Andre Schleife" [schleife- -illinois.edu] Dear Colleagues, The abstract submission deadline for the APS March Meeting (March 4-8, 2019; Boston, MA) is coming up (Friday, 10/26), hence a quick reminder: Please consider submitting your abstract to the Focus Topic "First-principles Modeling of Excited-State Phenomena in Materials", organized by Serdar Ogut (UIC), Yuan Ping (UC Santa Cruz), Sahar Sharifzadeh (Boston University), and myself (UIUC). It is cross-listed in DCOMP, DCP, DMP as 16.1.4, 5.1.7, 36.16.1.4. This is also a continuation of the 2018 focus topic (and before) with the same name. Last year we had the biggest attendance this far, which led to many stimulating discussions and we would like to continue this success in 2019! If you are working in these fields of research, please consider submitting your contributed abstract to our focus topic. A strong showing from the community will ensure the FT's success and continuity. Were looking forward to seeing many of you in Boston in March! FT description: Many properties of functional materials, interfaces, and nano-structures derive from electronic excitations. These processes determine properties such as ionization potential and electron affinity, optical spectra and exciton binding energies, electron-phonon coupling, charge transition levels, and energy level alignment at interfaces. In addition, hot carriers in semiconductors and nanostructures are generated, transition between excited states, transfer energy to the lattice, and recombine with each other. It is necessary to understand these properties from a fundamental point of view and to achieve design of materials with optimal performance for applications e.g., in transistors, light emitting diodes, solar cells, and photo-electrochemical cells. A proper description of electronic excitations requires theoretical approaches that go beyond ground state density functional theory (DFT). In recent years, Green's function based many-body perturbation theory methods like RPA, GW, and BSE have been adopted by a rapidly growing community of researchers in the field of computational materials physics. These have now become the de facto standard for the description of excited electronic states in solids and their surfaces. Ehrenfest dynamics and surface-hopping schemes, e.g. based on time-dependent DFT, are used to describe coupled electron-ion dynamics as the origin of interesting physics in photo-catalysis, surface chemical reactions, scintillators, or radiation shielding. Advances in high performance computing and scalable implementations in several popular electronic structure packages enable further progress. Sophisticated calculations are accessible for many users and feasible for large, complex systems with up to few hundred atoms. These methods are increasingly applied to interpret experiments, such as spectroscopies and femto-second pump-probe measurements, and to computationally design functional materials, interfaces, and nano-structures. This focus topic is dedicated to recent advances in many-body perturbation theory and electron-ion dynamics methods for electronic excitations: Challenges, scalable implementations in electronic structure codes, and applications to functional materials, interfaces, molecules, and nano-structures. It aims to attract researchers working on the nexus of electronic and optical properties of materials, hot electron dynamics, and device physics. With best regards, Serdar Ogut (University of Illinois, Chicago), Yuan Ping (UC Santa Cruz), Andre Schleife (UIUC), Sahar Sharifzadeh (Boston University) -- Andr Schleife Assistant Professor Department of Materials Science and Engineering University of Illinois, Urbana-Champaign Email: schleife===illinois.edu Phone: +1 (217) 244 0339 Web: http://schleife.matse.illinois.edu From owner-chemistry@ccl.net Sun Oct 21 05:54:01 2018 From: "Mark Andreww Zottola mzottola ~~ gmail.com" To: CCL Subject: CCL: How to visualize normal modes Message-Id: <-53516-181021055255-5132-cYJCuPKAY+6RCQXjqaQRbQ{=}server.ccl.net> X-Original-From: "Mark Andreww Zottola" Date: Sun, 21 Oct 2018 05:52:53 -0400 Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com] I can use any of a number of good visualization software to observe the normal modes from a qm calculation. However, if I want to generate a series of structures from that normal mode calculation, I receive the frequency, the intensity of the transition and a set of cartesian displacements. It is the last that I do not understand. Given the equilibrium geometry, what should I do to generate coordinate files? Are these vectors to be added together? Or are these meant to be a cross product? Perhaps something else? I just want to consider creating a multi-conformer file based on normal modes. I am simply looking for a direction in order to move forward. Thanks. From owner-chemistry@ccl.net Sun Oct 21 11:01:01 2018 From: "Brian Skinn brian.skinn-#-gmail.com" To: CCL Subject: CCL: How to visualize normal modes Message-Id: <-53517-181021084408-6232-arbLvD3a/wvgEhtc4/mcAA!A!server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary="000000000000b49ad20578bc7d27" Date: Sun, 21 Oct 2018 08:43:51 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn(-)gmail.com] --000000000000b49ad20578bc7d27 Content-Type: text/plain; charset="UTF-8" Mark, The Cartesian displacements given for each mode are basically a column vector of 3N values that can be added to the length-3N column vector of the Cartesian geometry to obtain a displaced position along the particular mode. Just scale the displacement vector by various suitable amounts (positive *and* negative values) to obtain different positions along the mode. There is a substantial catch, however: sometimes the displacements are reported in "mass-weighted" terms, and sometimes they're reported in "pure Cartesian" terms. see my Chemistry Stack Exchange answer here ( https://chemistry.stackexchange.com/questions/74923) for more context. In short, the physics of normal mode analysis are such that the motion of each atom is "most natural" when the distances involved in that motion are multiplied by the square root of the mass of that atom. (See Eqs. (1), (6)-(8) and surrounding discussion at the above Chem.SE link.) Thus, the triplet of x/y/z values within a given Cartesian displacement vector corresponding to each atom *may* need to be *divided* by the square root of that atom's mass before using the vector to generate displaced geometries. The quickest test I can think of for whether this rescaling is required for displacements provided by a given software package is to run a frequencies calculation on a heterodiatomic, such as HCl. If the magnitudes of the displacements are identical for the two atoms, then you *do* need to rescale. -Brian On Sun, Oct 21, 2018 at 7:08 AM Mark Andreww Zottola mzottola ~~ gmail.com < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com] > I can use any of a number of good visualization software to observe the > normal > modes from a qm calculation. However, if I want to generate a series of > structures from that normal mode calculation, I receive the frequency, the > intensity of the transition and a set of cartesian displacements. > > It is the last that I do not understand. Given the equilibrium geometry, > what > should I do to generate coordinate files? Are these vectors to be added > together? Or are these meant to be a cross product? Perhaps something > else? > > I just want to consider creating a multi-conformer file based on normal > modes. > I am simply looking for a direction in order to move forward. > > Thanks.> > > --000000000000b49ad20578bc7d27 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Mark,

The Cartesian displacements given for e= ach mode are basically a column vector of 3N values that can be added to th= e length-3N column vector of the Cartesian geometry to obtain a displaced p= osition along the particular mode.=C2=A0 Just scale the displacement vector= by various suitable amounts (positive *and* negative values) to obtain dif= ferent positions along the mode.

There is a substantial = catch, however: sometimes the displacements are reported in "mass-weig= hted" terms, and sometimes they're reported in "pure Cartesia= n" terms. see my Chemistry Stack Exchange answer here (https://chemistry.stackexc= hange.com/questions/74923) for more context.=C2=A0 In short, the physic= s of normal mode analysis are such that the motion of each atom is "mo= st natural" when the distances involved in that motion are multiplied = by the square root of the mass of that atom. (See Eqs. (1), (6)-(8) and sur= rounding discussion at the above Chem.SE link.) Thus, the triplet of x/y/z = values within a given Cartesian displacement vector corresponding to each a= tom *may* need to be *divided* by the square root of that atom's mass b= efore using the vector to generate displaced geometries.

The quickest test I can think of for whether this rescaling is requi= red for displacements provided by a given software package is to run a freq= uencies calculation on a heterodiatomic, such as HCl.=C2=A0 If the magnitud= es of the displacements are identical for the two atoms, then you *do* need= to rescale.

-Brian


On Sun, Oct 2= 1, 2018 at 7:08 AM Mark Andreww Zottola mzottola ~~ gmail.com <owner-chemistry*ccl.net> wrote:

Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com]
I can use any of a number of good visualization software to observe the nor= mal
modes from a qm calculation.=C2=A0 However, if I want to generate a series = of
structures from that normal mode calculation, I receive the frequency, the =
intensity of the transition and a set of cartesian displacements.

It is the last that I do not understand.=C2=A0 Given the equilibrium geomet= ry, what
should I do to generate coordinate files?=C2=A0 Are these vectors to be add= ed
together?=C2=A0 Or are these meant to be a cross product? Perhaps something= else?

I just want to consider creating a multi-conformer file based on normal mod= es.
=C2=A0I am simply looking for a direction in order to move forward.=C2=A0 <= br>
Thanks.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--000000000000b49ad20578bc7d27-- From owner-chemistry@ccl.net Sun Oct 21 11:35:01 2018 From: "Steve Williams willsd- -appstate.edu" To: CCL Subject: CCL:G: How to visualize normal modes Message-Id: <-53518-181021110802-29954-c7YHq2x+tZmx3E9r2fj8rA[a]server.ccl.net> X-Original-From: Steve Williams Content-Type: multipart/alternative; boundary="0000000000005090000578be8068" Date: Sun, 21 Oct 2018 11:07:44 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd!=!appstate.edu] --0000000000005090000578be8068 Content-Type: text/plain; charset="UTF-8" I wrote a program a long time ago that read the equilibrium cartesian coordinates and cartesian displacements from a modified gaussian output file, that would then generate a series of displaced geometries by adding something like -1.0*displaced x coord to equilibrium x coord and so on for all coords of all atoms, then -0.90*displaced x coord to equilibrium x coord, through 0.10**d*displaced x coord to equilibrium x to 1.0**displaced x coord to equilibrium x coord and so generate 21 new structures each with a different displacement along the selected normal mode. I used an ancient vizualization tool called xmol to animate these. I do recall there was some small controversy about how the displacements that gaussian printed out were normalized, but I am no linger sure of the details on this. There is a small chance I still have this fortran code somewhere but it has been more or less 20 years ago. Steve Williams On Sun, Oct 21, 2018 at 7:05 AM Mark Andreww Zottola mzottola ~~ gmail.com < owner-chemistry .. ccl.net> wrote: > > Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com] > I can use any of a number of good visualization software to observe the > normal > modes from a qm calculation. However, if I want to generate a series of > structures from that normal mode calculation, I receive the frequency, the > intensity of the transition and a set of cartesian displacements. > > It is the last that I do not understand. Given the equilibrium geometry, > what > should I do to generate coordinate files? Are these vectors to be added > together? Or are these meant to be a cross product? Perhaps something > else? > > I just want to consider creating a multi-conformer file based on normal > modes. > I am simply looking for a direction in order to move forward. > > Thanks.> > > --0000000000005090000578be8068 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I wrote a program a long= time ago that read the equilibrium cartesian coordinates and cartesian dis= placements from a modified gaussian output file, that would then generate a= series of displaced geometries by adding something like -1.0*displaced x c= oord to equilibrium x coord and so on for all coords of all atoms, then -0.= 90*displaced x coord to equilibrium x coord, through 0.10**d*displaced x co= ord to equilibrium x to 1.0**displaced x coord to equilibrium x coord and s= o generate 21 new structures each with a different displacement along the s= elected normal mode. I used an ancient vizualization tool called xmol to an= imate these. I do recall there was some small controversy about how the dis= placements that gaussian printed out were normalized, but I am no linger su= re of the details on this.=C2=A0 There is a small chance I still have this = fortran code somewhere but it has been more or less 20 years ago.
Steve Williams

On Sun, Oct 21, 2018 at 7:05 AM Mark Andreww Zottola mzottola ~~ gmail.com <owner-chemistry .. ccl.net> wrote:

Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com]
I can use any of a number of good visualization software to observe the nor= mal
modes from a qm calculation.=C2=A0 However, if I want to generate a series = of
structures from that normal mode calculation, I receive the frequency, the =
intensity of the transition and a set of cartesian displacements.

It is the last that I do not understand.=C2=A0 Given the equilibrium geomet= ry, what
should I do to generate coordinate files?=C2=A0 Are these vectors to be add= ed
together?=C2=A0 Or are these meant to be a cross product? Perhaps something= else?

I just want to consider creating a multi-conformer file based on normal mod= es.
=C2=A0I am simply looking for a direction in order to move forward.=C2=A0 <= br>
Thanks.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY .. ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST .. ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--0000000000005090000578be8068-- From owner-chemistry@ccl.net Sun Oct 21 14:15:00 2018 From: "Jens Spanget-Larsen spanget],[ruc.dk" To: CCL Subject: CCL:G: SV: CCL:G: How to visualize normal modes Message-Id: <-53519-181021141403-13820-NdopeChUVFi4TjkXX+YN4w]=[server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Language: da-DK Content-Type: multipart/alternative; boundary="_000_A94E15A372E6194CA8719D62642F6744013749E867MBX2adrucdk_" Date: Sun, 21 Oct 2018 18:13:54 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget:ruc.dk] --_000_A94E15A372E6194CA8719D62642F6744013749E867MBX2adrucdk_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mark, I have a program written in GWBASIC, similar to the one described by Steve.= If you are interested, contact me! Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget_._ruc.dk DK-4000 Roskilde, Denmark Web: thiele.ruc.dk/~spanget ------------------------------------------------------ ________________________________ Fra: owner-chemistry+spanget=3D=3Druc.dk_._ccl.net [owner-chemistry+spanget= =3D=3Druc.dk_._ccl.net] p=E5 vegne af Steve Williams willsd- -appstate.edu [o= wner-chemistry_._ccl.net] Sendt: 21. oktober 2018 17:07 Til: Jens Spanget-Larsen Emne: CCL:G: How to visualize normal modes I wrote a program a long time ago that read the equilibrium cartesian coord= inates and cartesian displacements from a modified gaussian output file, th= at would then generate a series of displaced geometries by adding something= like -1.0*displaced x coord to equilibrium x coord and so on for all coord= s of all atoms, then -0.90*displaced x coord to equilibrium x coord, throug= h 0.10**d*displaced x coord to equilibrium x to 1.0**displaced x coord to e= quilibrium x coord and so generate 21 new structures each with a different = displacement along the selected normal mode. I used an ancient vizualizatio= n tool called xmol to animate these. I do recall there was some small contr= oversy about how the displacements that gaussian printed out were normalize= d, but I am no linger sure of the details on this. There is a small chance= I still have this fortran code somewhere but it has been more or less 20 y= ears ago. Steve Williams On Sun, Oct 21, 2018 at 7:05 AM Mark Andreww Zottola mzottola ~~ gmail.com<= http://gmail.com> > wrote: Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com] I can use any of a number of good visualization software to observe the nor= mal modes from a qm calculation. However, if I want to generate a series of structures from that normal mode calculation, I receive the frequency, the intensity of the transition and a set of cartesian displacements. It is the last that I do not understand. Given the equilibrium geometry, w= hat should I do to generate coordinate files? Are these vectors to be added together? Or are these meant to be a cross product? Perhaps something else= ? I just want to consider creating a multi-conformer file based on normal mod= es. I am simply looking for a direction in order to move forward. Thanks. -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY###ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST###ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_A94E15A372E6194CA8719D62642F6744013749E867MBX2adrucdk_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Mark,

 

I have a program written in GWBASIC, similar to the one described by Ste= ve. If you are interested, contact me!

 

Yours, Jens >--<

     &nb= sp;            =             &nb= sp;            =             &nb= sp;  

  --= ----------------------------------------------------

  JENS SPANGET-LARSEN   &= nbsp;    Office:       +45= 4674 2710

  Dept. of Science   &nbs= p;       Fax:     &n= bsp;    +45 4674 3011

  Roskilde University   &= nbsp;    Mobile:       +45= 2320 6246

  P.O.Box 260    &nb= sp;           E-Mail:&nbs= p;     spanget_._ruc.dk=

  DK-4000 Roskilde, Denmark  W= eb: thiele.ruc.dk/~spanget

  --------------------------------------= ----------------

 

Fra: owner-chemistry+spanget=3D=3Druc.= dk_._ccl.net [owner-chemistry+spanget=3D=3Druc.dk_._ccl.net] p=E5 vegne af = Steve Williams willsd- -appstate.edu [owner-chemistry_._ccl.net]
Sendt: 21. oktober 2018 17:07
Til: Jens Spanget-Larsen
Emne: CCL:G: How to visualize normal modes

I wrote a program a long time ago that read the equilibriu= m cartesian coordinates and cartesian displacements from a modified gaussia= n output file, that would then generate a series of displaced geometries by= adding something like -1.0*displaced x coord to equilibrium x coord and so on for all coords of all atoms, then= -0.90*displaced x coord to equilibrium x coord, through 0.10**d*displaced = x coord to equilibrium x to 1.0**displaced x coord to equilibrium x coord a= nd so generate 21 new structures each with a different displacement along the selected normal mode. I used = an ancient vizualization tool called xmol to animate these. I do recall the= re was some small controversy about how the displacements that gaussian pri= nted out were normalized, but I am no linger sure of the details on this.  There is a small chance I = still have this fortran code somewhere but it has been more or less 20 year= s ago.
Steve Williams

On Sun, Oct 21, 2018 at 7:05 AM Mark Andreww Zottola mzott= ola ~~ gmail.com <owner-chemistry###ccl.net> wrote:<= br>

Sent to CCL by: "Mark Andreww Zottola" [mzottola]|[gmail.com]
I can use any of a number of good visualization software to observe the nor= mal
modes from a qm calculation.  However, if I want to generate a series = of
structures from that normal mode calculation, I receive the frequency, the =
intensity of the transition and a set of cartesian displacements.

It is the last that I do not understand.  Given the equilibrium geomet= ry, what
should I do to generate coordinate files?  Are these vectors to be add= ed
together?  Or are these meant to be a cross product? Perhaps something= else?

I just want to consider creating a multi-conformer file based on normal mod= es.
 I am simply looking for a direction in order to move forward.  <= br>
Thanks.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY###ccl.net or use:
     

E-mail to administrators: CHEMISTRY-REQUEST###ccl.net or use
     
     

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
     

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--_000_A94E15A372E6194CA8719D62642F6744013749E867MBX2adrucdk_-- From owner-chemistry@ccl.net Sun Oct 21 14:49:01 2018 From: "Geoffrey Hutchison geoff.hutchison.,.gmail.com" To: CCL Subject: CCL: How to visualize normal modes Message-Id: <-53520-181021142719-18243-SEoj7X5InyIVFMgxC2gxYw,server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_5B754481-9EEF-4362-9C14-EBB91A7970E4" Date: Sun, 21 Oct 2018 14:27:11 -0400 Mime-Version: 1.0 (Mac OS X Mail 12.0 \(3445.100.39\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison]|[gmail.com] --Apple-Mail=_5B754481-9EEF-4362-9C14-EBB91A7970E4 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii > I just want to consider creating a multi-conformer file based on = normal modes.=20 > I am simply looking for a direction in order to move forward. =20 Other answers have been excellent particularly on the caveat of knowing = if your program is writing mass-weighted or "pure" Cartesian = displacements. One suggestion - I'd highly suggest you look at the Python cclib = package: http://cclib.github.io I uploaded some scripts along this line (generate 100 random conformers = based on normal modes from a frequency calculation) here: https://gist.github.com/ghutchis/4721ba55b695afd1df84423e2b495719 = The scripts may be incomplete - I grabbed what I think are the needed = files from my "Scripts" directory. :-) They rely on cclib and Open Babel = python packages being installed. Even if they don't quite work, I = suspect they should give you (and others) a good starting point. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh-*-pitt.edu twitter: -*-ghutchis web: https://hutchison.chem.pitt.edu/= --Apple-Mail=_5B754481-9EEF-4362-9C14-EBB91A7970E4 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
I just want to consider creating a multi-conformer file based = on normal modes.
I am simply looking for a direction in = order to move forward.  

Other answers have been excellent particularly on the caveat = of knowing if your program is writing mass-weighted or "pure" Cartesian = displacements.

One suggestion - I'd highly suggest you look at the Python = cclib package:
http://cclib.github.io

I uploaded some scripts along this line = (generate 100 random conformers based on normal modes from a frequency = calculation) here:
https://gist.github.com/ghutchis/4721ba55b695afd1df84423e2b4957= 19

The = scripts may be incomplete - I grabbed what I think are the needed files = > from my "Scripts" directory. :-) They rely on cclib and Open Babel = python packages being installed. Even if they don't quite work, I = suspect they should give you (and others) a good starting = point.

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of = Pittsburgh
tel: (412) 648-0492
email: = geoffh-*-pitt.edu
twitter: -*-ghutchis
web: https://hutchison.chem.pitt.edu/
= --Apple-Mail=_5B754481-9EEF-4362-9C14-EBB91A7970E4--