Recommendations for DFT/computational chemistry software?

older
Lecture/tutorials required on FeFF...

Scott Calvin

12 Aug 2013 12 Aug '13

1:30 p.m.

Hi all, I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose? --Scott Calvin Sarah Lawrence College

Show replies by date

Paul Fons

16 Aug 16 Aug

2:27 p.m.

New subject: Recommendations for DFT/computational chemistry software?

Hi Scott, I have been dabbling in DFT for a while. There are many free packages around, but if you would like to model XAFS as well, I would suggest an all electron code for accuracy (such as Wien2K). For general purposes, I am also using VASP and CASTEP. The former uses projector augmented waves and the other ultrasoft pseudopotentials. VASP is fast and scalable to the largest machines and is designed from the ground up for quantum molecular dynamics. Both VASP and CASTEP use pseudopotentials whereas Wien2K uses a linearized augmented plane wave basis (read as radial wavefunctions and Ylms in a sphere about each atom and plane waves between spheres with boundary condition matching at the surface of the spheres. This way it is possible to model even the 1s electrons for heavier atoms and yes it does affect valence electron wavefunctions via orthogonality. All of these approaches are single particle DFT approaches, but it should be good enough for a start, if you want to go beyond these, with solutions of the Bethe-Saltpeter equation (electron and a hole) things get complicated and expensive (in terms of computer time) very quickly. If you are interested in free software I would suggest gpaw, quantum espresso, and abinit. I would also suggest learning the atomic simulation environment in which you can program multiple codes in python (and even solve for maximally localized Wannier functions in a few lines of code!) (Atomic Simulation Environment — ASE 3.8.0.3329 documentation). What exactly are you trying to do? If you are looking for a non-spherical approximation for EXAFS beyond feff8's spheres, you might try FNDMES by Joly as well. Cheers, Paul On Aug 12, 2013, at 10:30 PM, Scott Calvin wrote:

...

Hi all,

I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose?

--Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Chief Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

Matthew Marcus

4:45 p.m.

New subject: Recommendations for DFT/computational chemistry software?

Please correct me if I'm wrong, but I get the impression that if you don't know exactly what you're doing, these programs will cheerfully return wrong answers. There seem to be many parameters and choices to be made. I once looked at Quantum Espresso but gave up when I saw that the script for doing MD on a single water molecule ran for over a page of incomprehensible code. I didn't see anything that looked like a step-by-step tutorial or manual. Gaussian with the Gaussview UI is simple enough for an experimentalist like me to use; are there better packages out there which are as well? I also get the impression that you need some pretty hefty compute power. A Linux system is probably to be preferred over Windows. One of these days I should learn Python, not just for this stuff. mam On 8/16/2013 7:27 AM, Paul Fons wrote:

...

Hi Scott, I have been dabbling in DFT for a while. There are many free packages around, but if you would like to model XAFS as well, I would suggest an all electron code for accuracy (such as Wien2K). For general purposes, I am also using VASP and CASTEP. The former uses projector augmented waves and the other ultrasoft pseudopotentials. VASP is fast and scalable to the largest machines and is designed from the ground up for quantum molecular dynamics. Both VASP and CASTEP use pseudopotentials whereas Wien2K uses a linearized augmented plane wave basis (read as radial wavefunctions and Ylms in a sphere about each atom and plane waves between spheres with boundary condition matching at the surface of the spheres. This way it is possible to model even the 1s electrons for heavier atoms and yes it does affect valence electron wavefunctions via orthogonality. All of these approaches are single particle DFT approaches, but it should be good enough for a start, if you want to go beyond these, with solutions of the Bethe-Saltpeter equation (electron and a hole) things get complicated and expensive (in terms of computer time) very quickly.

If you are interested in free software I would suggest gpaw, quantum espresso, and abinit. I would also suggest learning the atomic simulation environment in which you can program multiple codes in python (and even solve for maximally localized Wannier functions in a few lines of code!) (Atomic Simulation Environment — ASE 3.8.0.3329 documentation https://www.google.co.jp/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CC8QFjAA&url=https://wiki.fysik.dtu.dk/ase/&ei=WDYOUs2vBsaHkwX3h4H4Cg&usg=AFQjCNGJtTBmzvPVE0wgaKpLivT6K59Whw&bvm=bv.50768961,d.dGI).

What exactly are you trying to do? If you are looking for a non-spherical approximation for EXAFS beyond feff8's spheres, you might try FNDMES by Joly as well.

Cheers, Paul

On Aug 12, 2013, at 10:30 PM, Scott Calvin mailto:scalvin@sarahlawrence.edu> wrote:

...
Hi all,

I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose?

--Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Chief Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI

AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568

tel. +81-298-61-5636 fax. +81-298-61-2939

email: _paul-fons@aist.go.jp mailto:paul-fons@aist.go.jp_

The following lines are in a Japanese font

〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Paul Fons

23 Aug 23 Aug

1:11 a.m.

New subject: Recommendations for DFT/computational chemistry software?

Hi Matthew, You are absolutely correct in that the old adage still applies, "garbage in equals garbage out". There is no substitute for knowing what you are doing. On the other hand, the great increases in computer power have made what was a nearly intractable problem much more manageable and it is a distinct advantage to be able to use ab-initio software to get insight into the chemistry. Of course, the scaling problem with plane-wave DFT is still there (memory = cube of the number of atoms), but even on a Mac Pro with 32 GB of memory you can simulate the ground state of hundreds of atoms in reasonable times whereas ten years ago, you would have had to use a supercomputer for the same problem. The codes themselves are much easier to use and their associated mailing lists make it a great way to learn the details of a given calculation. It certainly beats writing your own code from scratch (which I did back in 1990 when I was at the Univ. of Illinois on the NCSA machines)! On the other hand, I realize that I should have recommended a couple of books for background reading. A relatively easy read on solid state physics including some details of DFT Efthimios Kaxiras: "Atomic and Electronic Structure of Solids" My favourite book is a more comprehensive work. Richard M. Martin: "Electronic Structure: Basic Theory and Practical Methods" I should also add that abinit (http://www.abinit.org) is a free (as in gnu copyleft) code that has a set of very nice tutorials online starting with bonding two hydrogen atoms with references to appropriate papers to read for deeper information. To summarize, my point is that the hardware/software barriers to using DFT codes have gotten much smaller over the years and then investing the time in learning them can potentially offer greater insight into hard to understand problems. It is certainly useful for EXAFS in that one can obtain the relaxed structures in a 0 K calculation to compare for instance different possible XANES structures while at the same time potentially offering calculated material properties (optical reflectivity, Raman, etc.) that can offer additional results that can be compared to experiment. Certainly the ASE environment allows one to program a series of calculations using python and helps shorten the time necessary for writing input files and keeping track of the voluminous output. I give all of my postdocs extensive training in using DFT to get insight into material science problems. While it is not always useful, it can provide useful information in many cases. Paul On Aug 17, 2013, at 1:45 AM, Matthew Marcus wrote:

...

Please correct me if I'm wrong, but I get the impression that if you don't know exactly what you're doing, these programs will cheerfully return wrong answers. There seem to be many parameters and choices to be made. I once looked at Quantum Espresso but gave up when I saw that the script for doing MD on a single water molecule ran for over a page of incomprehensible code. I didn't see anything that looked like a step-by-step tutorial or manual. Gaussian with the Gaussview UI is simple enough for an experimentalist like me to use; are there better packages out there which are as well?

I also get the impression that you need some pretty hefty compute power. A Linux system is probably to be preferred over Windows.

One of these days I should learn Python, not just for this stuff. mam

On 8/16/2013 7:27 AM, Paul Fons wrote:

...
Hi Scott, I have been dabbling in DFT for a while. There are many free packages around, but if you would like to model XAFS as well, I would suggest an all electron code for accuracy (such as Wien2K). For general purposes, I am also using VASP and CASTEP. The former uses projector augmented waves and the other ultrasoft pseudopotentials. VASP is fast and scalable to the largest machines and is designed from the ground up for quantum molecular dynamics. Both VASP and CASTEP use pseudopotentials whereas Wien2K uses a linearized augmented plane wave basis (read as radial wavefunctions and Ylms in a sphere about each atom and plane waves between spheres with boundary condition matching at the surface of the spheres. This way it is possible to model even the 1s electrons for heavier atoms and yes it does affect valence electron wavefunctions via orthogonality. All of these approaches are single particle DFT approaches, but it should be good enough for a start, if you want to go beyond these, with solutions of the Bethe-Saltpeter equation (electron and a hole) things get complicated and expensive (in terms of computer time) very quickly.

If you are interested in free software I would suggest gpaw, quantum espresso, and abinit. I would also suggest learning the atomic simulation environment in which you can program multiple codes in python (and even solve for maximally localized Wannier functions in a few lines of code!) (Atomic Simulation Environment — ASE 3.8.0.3329 documentation https://www.google.co.jp/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CC8QFjAA&url=https://wiki.fysik.dtu.dk/ase/&ei=WDYOUs2vBsaHkwX3h4H4Cg&usg=AFQjCNGJtTBmzvPVE0wgaKpLivT6K59Whw&bvm=bv.50768961,d.dGI).

What exactly are you trying to do? If you are looking for a non-spherical approximation for EXAFS beyond feff8's spheres, you might try FNDMES by Joly as well.

Cheers, Paul

On Aug 12, 2013, at 10:30 PM, Scott Calvin mailto:scalvin@sarahlawrence.edu> wrote:

...
Hi all,

I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose?

--Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Chief Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI

AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568

tel. +81-298-61-5636 fax. +81-298-61-2939

email: _paul-fons@aist.go.jp mailto:paul-fons@aist.go.jp_

The following lines are in a Japanese font

〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所ナノエレクトロニクス研究部門相変化新規機能デバイス研究チーム上級主究員ポール・フォンス

Matthew Marcus

16 Aug 16 Aug

4:53 p.m.

New subject: crystal analyzer and microprobe

I know that this is somewhat off-topic, but the list reaches all the right people. I have some collaborators who are looking to measure the Ni/Fe ratio is particles of Fe-rich material. This ratio is << 1, and they need a non-destructive probe. A microprobe with a crystal analyzer would do the job nicely. Here at ALS, we have the microprobe, but not the analyzer. Can anyone recommend a beamline that has both? I'm pretty sure there's at least one at APS; a beamline number and a name would help a lot. Thanks. mam

Matt Newville

6:04 p.m.

New subject: crystal analyzer and microprobe

Hi Matthew, On Aug 16, 2013 11:53 AM, "Matthew Marcus" wrote:

...

I know that this is somewhat off-topic, but the list reaches all the

right people. I have some collaborators who are looking to measure

...

the Ni/Fe ratio is particles of Fe-rich material. This ratio is << 1, and they need a non-destructive probe. A microprobe with a crystal analyzer would do the job nicely. Here at ALS, we have the microprobe, but not the analyzer. Can anyone recommend a beamline that has both? I'm pretty sure there's at least one at APS; a beamline number and a name would help a lot. Thanks. mam _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Both GSE (13 IDE) and PNC (20 IDC) have wavelength dispersive spectrometers that could work. Was the idea to get an absolute ratio? That can be challenging for large dynamic ranges with any detector, but can be done. --Matt

Matthew Marcus

6:36 p.m.

New subject: crystal analyzer and microprobe

Yup, the idea is indeed to get an absolute ratio. Not only that, but these are particles of size greater than the absorption depth of the Ni fluorescence in the Fe matrix, but not MUCH greater. The approach we've taken here is to plot the count ratio va. Fe counts as we move on the sample, and extrapolate to 0 counts. I'll pass the info to the interested parties. mam On 8/16/2013 11:04 AM, Matt Newville wrote:

...

Hi Matthew,

On Aug 16, 2013 11:53 AM, "Matthew Marcus" mailto:mamarcus@lbl.gov> wrote:

...
I know that this is somewhat off-topic, but the list reaches all the right people. I have some collaborators who are looking to measure the Ni/Fe ratio is particles of Fe-rich material. This ratio is << 1, and they need a non-destructive probe. A microprobe with a crystal analyzer would do the job nicely. Here at ALS, we have the microprobe, but not the analyzer. Can anyone recommend a beamline that has both? I'm pretty sure there's at least one at APS; a beamline number and a name would help a lot. Thanks. mam _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Both GSE (13 IDE) and PNC (20 IDC) have wavelength dispersive spectrometers that could work. Was the idea to get an absolute ratio? That can be challenging for large dynamic ranges with any detector, but can be done.

--Matt

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Ashley Norris

7:15 p.m.

New subject: crystal analyzer and microprobe

Something to consider would be modelling the entire thing in Penepma. In theory you could create a lookup table of observed ratios vs actual ratios, and then use that once you take your measurements to try to get back to the actual ratio. I'm replying to you directly because it's Friday afternoon and I'm worried that I may have misunderstood something about your question. Regards, Ash PS: Some links to get you started, if not already familiar with Penepma. http://www.geology.wisc.edu/~johnf/AGU-2007_JHF.pdf http://pypenelope.sourceforge.net/code/penelopetools/api/program/penepma.htm... http://www.probesoftware.com/Technical.htm On 16/08/2013 19:36, Matthew Marcus wrote:

...

Yup, the idea is indeed to get an absolute ratio. Not only that, but these are particles of size greater than the absorption depth of the Ni fluorescence in the Fe matrix, but not MUCH greater. The approach we've taken here is to plot the count ratio va. Fe counts as we move on the sample, and extrapolate to 0 counts. I'll pass the info to the interested parties. mam

On 8/16/2013 11:04 AM, Matt Newville wrote:

...
Hi Matthew,

On Aug 16, 2013 11:53 AM, "Matthew Marcus" mailto:mamarcus@lbl.gov> wrote:

...
I know that this is somewhat off-topic, but the list reaches all

...
the Ni/Fe ratio is particles of Fe-rich material. This ratio is << 1, and they need a non-destructive probe. A microprobe with a crystal analyzer would do the job nicely. Here at ALS, we have the microprobe, but not the analyzer. Can anyone recommend a beamline

the right people. I have some collaborators who are looking to measure that has both?

...
I'm pretty sure there's at least one at APS; a beamline number and a name would help a lot. Thanks. mam _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Both GSE (13 IDE) and PNC (20 IDC) have wavelength dispersive spectrometers that could work. Was the idea to get an absolute ratio? That can be challenging for large dynamic ranges with any detector, but can be done.

--Matt

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- --- Ashley Norris Department of Earth Sciences South Parks Road, Oxford, UK ----------------

Scott Calvin

19 Aug 19 Aug

12:40 a.m.

Thanks, all, for the suggestions and advice! --Scott Calvin Sarah Lawrence College On Aug 12, 2013, at 9:30 AM, Scott Calvin wrote:

...

Hi all,

I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose?

--Scott Calvin Sarah Lawrence College _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

4091

Age (days ago)

4102

Last active (days ago)

List overview

Download

8 comments

5 participants

participants (5)

Ashley Norris
Matt Newville
Matthew Marcus
Paul Fons
Scott Calvin