CCL:G: Chargemol 3.0 released
- From: "Salter-Duke, Brian James -"
<brian.james.duke:gmail.com>
- Subject: CCL:G: Chargemol 3.0 released
- Date: Sun, 22 Jun 2014 10:37:09 +1000
Sent to CCL by: "Salter-Duke, Brian James -"
[brian.james.duke]=[gmail.com]
I agree with Alex. If EDFs are included in the .wfx file, might it not
cause problems if that file is used by a program other than Chargemol.
I also agree that the .wfx format could be implemented in GAMESS. I am a
developer of VB2000 which is included in GAMESS, so I will talk to Mike
Schmidt in the Gordon Group about this.
Brian.
On Sun, Jun 22, 2014 at 12:46:54AM +0400, Alex A. Granovsky
gran(!)classic.chem.msu.su wrote:
> Hi Tom,
>
> Frankly I do not understand why should we incorporate EDFs into Firefly.
>
> EDFs is an approximation which does not take into account effects due to
core-valence polarization and intimate details of the ECPs in use. It is only
useful to perform approximate AIM analysis with ECPs.
>
> If one wants to use, say, Chargemol in conjunction with Firefly, it would
be logical if EDFs will be provided by Chargemol as these are not the data
computed within the particular QC run.
>
> With no EDF data, .wfx format is pretty similar to .wfn and could be
implemented.
>
> Kind regards,
> Alex Granovsky
>
>
> > From: Thomas Manz thomasamanz]~[gmail.com
> Sent: Saturday, June 21, 2014 6:56 PM
> To: Granovsky, Alex, A.
> Subject: CCL:G: Chargemol 3.0 released
>
> Hi Brian,
>
> >Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can
> > only use HF or DFT densities as it calculated them from the MOs (KS
> > orbitals)? Would it need something that outputs the full density
matrix
> > to use CASSCF results?
>
>
>
> The Chargemol program can use input from any quantum chemistry method (DFT,
HF, CASSCF, MP2, coupled-cluster, etc.).
> Just include Density = Current, Output = WFX, Pop= NO (for spin unpolarized
calculation) or NOAB (for spin polarized calculation) on the GAUSSIAN 09 route
line and the name of the .wfx file at the bottom of the GAUSSIAN input (.com or
.gjf) file. This directs GAUSSIAN 09 to output the fully correlated density to
the .WFX file, so you will get the corresponding density when running methods
like DFT, HF, CASSCF, MP2, coupled-cluster, etc.
>
>
> > Does anyone have any idea how it could use output from GAMESS(US) [or
> > indeed GAMESS(UK) or Firefly]?
>
>
>
> Best route in the long run would be for GAMESS and Firefly developers to
add code to output .wfx file. The .wfx files are read by AIMALL, MultiWFN, and
Chargemol programs that perform various kinds of atomic population analysis. The
.wfx format specification is shown at http://aim.tkgristmill.com/wfxformat.html The .wfx file
contains information about the cartesian Gaussian basis set primitives, the
basis set coefficients for the natural orbitals (eigenvectors of the first-order
density matrix), positions of each atom, system net charge and total number of
electrons, nuclear charges, and core electrons replaced by effective core
potentials (if any). For quantum chemistry calculations that used effective core
potentials, the .wfx file contains Electron Density Functions (EDFs), which are
normally spherically symmetric for each atom, that specify the electron density
of the core electrons replaced by the atom's effective core potential.
>
>
> In principle, it should only take one person a few of days of programming
to add the option to output a .wfx file from the GAMESS or Firefly software
packages. Presumably, all of the information about the cartesian basis set
primitives, natural orbital basis set coefficients, nuclear positions, etc. is
already available within these programs and code just needs to be added to
output them in .wfx file format. The only information that may not be already
available within the GAMESS and Firefly codes is the EDFs that specify the
density of the core electrons replaced by effective core potentials. I have
generated a set of core electron densities for all elements atomic number 1 (H)
to 109 (Mt), so if one of the GAMESS or Firefly developers is in need of that
information, they can contact me and I can help them with a library of core
electron densities for the purpose of generating .wfx files.
>
>
> I recommend that you contact the GAMESS or Firefly developers and ask if it
is possible for them to add output of .wfx file format. This will certainly be
the best long-term solution.
>
> Sincerely,
>
> Tom Manz
> assistant professor, Chemical & Materials Engineering
> New Mexico State University
>
>
>
> On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke, Brian James
brian.james.duke() gmail.com <owner-chemistry-$-ccl.net> wrote:
>
> Sent to CCL by: "Salter-Duke, Brian James "
[brian.james.duke(_)gmail.com]
> This seems a really useful program.
>
> Does anyone have any idea how it could use output from GAMESS(US) [or
> indeed GAMESS(UK) or Firefly]?
>
> Am I correct in thinking that with GAUSSIAN 09 using .wfx files, it can
> only use HF or DFT densities as it calculated them from the MOs (KS
> orbitals)? Would it need something that outputs the full density matrix
> to use CASSCF results?
>
> Brian.
>
> On Mon, Jun 16, 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%nmsu.edu
wrote:
> > Hi,
> >
> > I just wanted to let everyone know about the release of Chargemol
> > version 3.0, which performs Density Derived Electrostatic and Chemical
> > (DDEC) atomic population analysis.
> >
> > The latest version has the following features:
> >
> > 1) Computes net atomic charges, atomic spin moments, and now effective
> > bond orders (EBOs) for nonperiodic and periodic materials. For each
atom,
> > the sum of effective bond orders (SEBO) is also computed and printed.
The
> > program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a
variety
> > of other quantum chemistry programs.
> >
> > 2) Atomic dipole and quadrupole moments are computed for all systems.
> > For nonperiodic materials, the total system dipole and quadrupole
moments
> > are also computed. The latest version adds the computation and
printing of
> > the traceless quadrupole tensor eigenvalues.
> >
> > 3) A new constraint has been added to improvement the treatment in
ionic
> > systems containing small cations. For example, it was noticed that in
> > crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too
> > contracted and too positively charged. This has been fixed by
constraining
> > the rate of decay of atomic weights to be no faster than exp(-3*r) in
> > regions where atoms overlap.
> >
> > 4) To improve the speed, the program has been translated from Matlab
> > into Fortran code. The Fortran code is parallelized with OpenMP
allowing it
> > to run on multiple processors with a shared memory (i.e., single
> > node, multiple processors). A serial version of the Fortran code is
also
> > available.
> >
> > 5) Precompiled Windows and Linux binaries and the uncompiled
sourcecode
> > are available. Many users can utilize the precompiled executables
> > without recompiling the program.
> >
> > 6) The program is free to download from ddec.sourceforge.net. The
> > download includes a manual explaining how to install and run the
program.
> >
> > Sincerely,
> >
> > Tom Manz
>
> --
> Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(a)monash.edu
> Adjunct Associate Professor
> Monash Institute of Pharmaceutical Sciences
> Monash University Parkville Campus, VIC 3052, Australia>
>
>
> E-mail to subscribers: CHEMISTRY-$-ccl.net or use:E-mail to administrators:
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> <HTML><HEAD></HEAD>
> <BODY dir=ltr>
> <DIV dir=ltr>
> <DIV style="FONT-FAMILY: 'Calibri'; COLOR: #000000; FONT-SIZE:
12pt">
> <DIV>Hi Tom,</DIV>
> <DIV> </DIV>
> <DIV>Frankly I do not understand why should we incorporate EDFs into
Firefly.
> </DIV>
> <DIV> </DIV>
> <DIV>EDFs is an approximation which does not take into account
effects due to
> core-valence polarization and intimate details of the ECPs in use. It is
only
> useful to perform approximate AIM analysis with ECPs. </DIV>
> <DIV> </DIV>
> <DIV>If one wants to use, say, Chargemol in conjunction with Firefly,
it would
> be logical if EDFs will be provided by Chargemol as these are not the data
> computed within the particular QC run. </DIV>
> <DIV> </DIV>
> <DIV>With no EDF data, .wfx format is pretty similar to
.wfn and could be
> implemented. </DIV>
> <DIV> </DIV>
> <DIV>Kind regards,</DIV>
> <DIV>Alex Granovsky</DIV>
> <DIV> </DIV>
> <DIV
> style="FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri';
COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION:
none">
> <DIV style="FONT: 10pt tahoma">
> <DIV><FONT size=3
face=Calibri></FONT> </DIV>
> <DIV style="BACKGROUND: #f5f5f5">
> <DIV style="font-color: black"><B>From:</B>
<A title=owner-chemistry^-^ccl.net
> href="mailto:owner-chemistry^-^ccl.net";>Thomas Manz
thomasamanz]~[gmail.com</A>
> </DIV>
> <DIV><B>Sent:</B> Saturday, June 21, 2014 6:56
PM</DIV>
> <DIV><B>To:</B> <A title=gran^-^classic.chem.msu.su
> href="mailto:gran^-^classic.chem.msu.su";>Granovsky, Alex,
A. </A> </DIV>
> <DIV><B>Subject:</B> CCL:G: Chargemol 3.0
released</DIV></DIV></DIV>
> <DIV> </DIV></DIV>
> <DIV
> style="FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri';
COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION:
none">
> <DIV dir=ltr>Hi Brian,
> <DIV> </DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">>Am I
> correct in thinking that with GAUSSIAN 09 using .wfx files, it
can</SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">> only use
> HF or DFT densities as it calculated them from the MOs
(KS</SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">>
> orbitals)? Would it need something that outputs the full density
> matrix</SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">> to use
> CASSCF results?</SPAN><BR></DIV>
> <DIV><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px"><BR></SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">The Chargemol
> program can use input from any quantum chemistry method (DFT, HF, CASSCF,
MP2,
> coupled-cluster, etc.).</SPAN></DIV>
> <DIV><FONT face="arial, sans-serif">Just include
Density = Current, Output =
> WFX, Pop= NO (for spin unpolarized calculation) or NOAB (for spin polarized
> calculation) on the GAUSSIAN 09 route line and the name of the .wfx file at
the
> bottom of the GAUSSIAN input (.com or .gjf) file. </FONT><FONT
> face="arial, sans-serif">This directs GAUSSIAN 09 to output
the fully correlated
> density to the .WFX file, so you will get the corresponding density when
running
> methods like </FONT><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">DFT,
HF, CASSCF, MP2,
> coupled-cluster, etc.</SPAN></DIV>
> <DIV><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px"><BR></SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">> Does
> anyone have any idea how it could use output from GAMESS(US)
[or</SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">> indeed
> GAMESS(UK) or Firefly]?</SPAN><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px"><BR></SPAN></DIV>
> <DIV><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px"><BR></SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif; FONT-SIZE:
13px">Best route in
> the long run would be for GAMESS and Firefly developers to add code to
output
> .wfx file. </SPAN><SPAN style="FONT-FAMILY:
arial,sans-serif">The .wfx files are
> read by AIMALL, MultiWFN, and Chargemol programs that perform various kinds
of
> atomic population analysis. </SPAN><SPAN
> style="FONT-FAMILY: arial,sans-serif; FONT-SIZE: 13px">The
.wfx format
> specification is shown at </SPAN><FONT face="arial,
sans-serif"><A
> href="http://aim.tkgristmill.com/wfxformat.html">http-:-//aim.tkgristmill.com/wfxformat.html</A>
> The .wfx file contains information about the cartesian Gaussian basis set
> primitives, the basis set coefficients for the natural orbitals
(eigenvectors of
> the first-order density matrix), positions of each atom, system net charge
and
> total number of electrons, nuclear charges, and core electrons replaced by
> effective core potentials (if any). For quantum chemistry calculations that
used
> effective core potentials, the .wfx file contains Electron Density
Functions
> (EDFs), which are normally spherically symmetric for each atom, that
specify the
> electron density of the core electrons replaced by the atom's effective
core
> potential. </FONT></DIV>
> <DIV><SPAN style="FONT-FAMILY:
arial,sans-serif"><BR></SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif">In
principle, it should only
> take one person a few of days of programming to add the option to output a
.wfx
> file from the GAMESS or Firefly software packages. Presumably, all of the
> information about the cartesian basis set primitives, natural orbital basis
set
> coefficients, nuclear positions, etc. is already available within these
> programs</SPAN><SPAN style="FONT-FAMILY:
arial,sans-serif"> and code just needs
> to be added to output them in .wfx file format. The only information that
may
> not be already available within the GAMESS and Firefly codes is the EDFs
that
> specify the density of the core electrons replaced by effective core
potentials.
> I have generated a set of core electron densities for all elements atomic
number
> 1 (H) to 109 (Mt), so if one of the GAMESS or Firefly developers is in need
of
> that information, they can contact me and I can help them with a library of
core
> electron densities for the purpose of generating .wfx
files.</SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY:
arial,sans-serif"><BR></SPAN></DIV>
> <DIV><SPAN style="FONT-FAMILY: arial,sans-serif">I
recommend that you contact
> the GAMESS or Firefly developers and ask if it is possible for them to add
> output of .wfx file format. This will certainly be the best long-term
solution.
> </SPAN></DIV>
> <DIV> </DIV>
> <DIV>Sincerely,</DIV>
> <DIV> </DIV>
> <DIV>Tom Manz</DIV>
> <DIV>assistant professor, Chemical & Materials
Engineering</DIV>
> <DIV>New Mexico State University</DIV></DIV>
> <DIV class=gmail_extra><BR><BR>
> <DIV class=gmail_quote>On Sat, Jun 21, 2014 at 1:34 AM, Salter-Duke,
Brian James
> brian.james.duke() <A href="http://gmail.com";>gmail.com</A> <SPAN
dir=ltr><<A
> href="mailto:owner-chemistry-$-ccl.net";
> target=_blank>owner-chemistry-$-ccl.net</A>></SPAN>
wrote:<BR><BR>Sent to CCL
> by: "Salter-Duke, Brian James " [brian.james.duke(_)<A
href="http://gmail.com";
> target=_blank>gmail.com</A>]<BR>This seems a really useful
program.<BR><BR>Does
> anyone have any idea how it could use output from GAMESS(US)
[or<BR>indeed
> GAMESS(UK) or Firefly]?<BR><BR>Am I correct in thinking that
with GAUSSIAN 09
> using .wfx files, it can<BR>only use HF or DFT densities as it
calculated them
> > from the MOs (KS<BR>orbitals)? Would it need something that
outputs the full
> density matrix<BR>to use CASSCF
results?<BR><BR>Brian.<BR><BR>On Mon, Jun 16,
> 2014 at 08:48:33PM -0600, Thomas Manz tmanz%x%<A href="http://nmsu.edu";
> target=_blank>nmsu.edu</A> wrote:<BR>>
Hi,<BR>><BR>> I just wanted to
> let everyone know about the release of Chargemol<BR>> version
3.0, which
> performs Density Derived Electrostatic and Chemical<BR>>
(DDEC) atomic
> population analysis.<BR>><BR>> The latest version
has the following
> features:<BR>><BR>> 1) Computes net atomic
charges, atomic spin moments,
> and now effective<BR>> bond orders (EBOs) for nonperiodic and
periodic
> materials. For each atom,<BR>> the sum of effective bond
orders (SEBO) is
> also computed and printed. The<BR>> program analyzes output
from GAUSSIAN 09
> (.wfx files), VASP, and a variety<BR>> of other quantum
chemistry
> programs.<BR>><BR>> 2) Atomic dipole and
quadrupole moments are computed
> for all systems.<BR>> For nonperiodic materials, the total
system dipole and
> quadrupole moments<BR>> are also computed. The latest version
adds the
> computation and printing of<BR>> the traceless quadrupole
tensor
> eigenvalues.<BR>><BR>> 3) A new constraint has
been added to improvement
> the treatment in ionic<BR>> systems containing small cations.
For example, it
> was noticed that in<BR>> crystals such as Na2Cl and Li-Ru-O,
the Na and Li
> atoms become too<BR>> contracted and too positively charged.
This has been
> fixed by constraining<BR>> the rate of decay of atomic weights
to be no
> faster than exp(-3*r) in<BR>> regions where atoms
overlap.<BR>><BR>> 4)
> To improve the speed, the program has been translated from
Matlab<BR>> into
> Fortran code. The Fortran code is parallelized with OpenMP allowing
it<BR>>
> to run on multiple processors with a shared memory (i.e.,
single<BR>> node,
> multiple processors). A serial version of the Fortran code is
also<BR>>
> available.<BR>><BR>> 5) Precompiled Windows and
Linux binaries and the
> uncompiled sourcecode<BR>> are available. Many users can
utilize the
> precompiled executables<BR>> without recompiling the
program.<BR>><BR>>
> 6) The program is free to download from <A href="http://ddec.sourceforge.net";
> target=_blank>ddec.sourceforge.net</A>. The<BR>>
download includes a manual
> explaining how to install and run the
program.<BR>><BR>>
> Sincerely,<BR>><BR>> Tom
Manz<BR><BR>--<BR> Brian Salter-Duke
> (Brian Duke) Brian.Salter-Duke(a)<A href="http://monash.edu";
>
target=_blank>monash.edu</A><BR>
> Adjunct Associate
>
Professor<BR>
> Monash Institute of Pharmaceutical
Sciences<BR>
> Monash University Parkville Campus, VIC 3052,
Australia<BR><BR><BR><BR>-= This
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--
Brian Salter-Duke (Brian Duke) Brian.Salter-Duke+/-monash.edu
Adjunct Associate Professor
Monash Institute of Pharmaceutical Sciences
Monash University Parkville Campus, VIC 3052, Australia