From owner-chemistry@ccl.net Mon Jul 10 07:14:00 2017 From: "Wendy A Warr wendy__warr.com" To: CCL Subject: CCL: Two free ChemAxon meeting reports Message-Id: <-52880-170710071226-28690-G2a39anfKjDUeqjnOtizCQ(_)server.ccl.net> X-Original-From: "Wendy A Warr" Date: Mon, 10 Jul 2017 07:12:24 -0400 Sent to CCL by: "Wendy A Warr" [wendy_._warr.com] A second report is now out. My report on the ChemAxon European Meeting held in Budapest in May is now on open access at https://www.chemaxon.com/library/chemaxon-european-user-meeting-budapest-may-9-11-2017/. The report on the US meeting was posted a month ago at https://www.chemaxon.com/library/chemaxon-us-user-meeting-san-francisco-april-10-11-2017/. Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 wendy-$-warr.com http://orcid.org/0000-0002-7064-4739 http://www.warr.com Skype: wendyannewarr Twitter: -$-WendyAnneWarr From owner-chemistry@ccl.net Mon Jul 10 12:57:00 2017 From: "Angelo Rossi angelo.raymond.rossi{=}gmail.com" To: CCL Subject: CCL:G: NWChem developers seeking your input Message-Id: <-52881-170710113529-6481-ll8b5Fz/qSHWSV0uwO2qEg]|[server.ccl.net> X-Original-From: Angelo Rossi Content-Type: multipart/alternative; boundary="001a11495ff6b75ef90553f854f2" Date: Mon, 10 Jul 2017 11:35:21 -0400 MIME-Version: 1.0 Sent to CCL by: Angelo Rossi [angelo.raymond.rossi*o*gmail.com] --001a11495ff6b75ef90553f854f2 Content-Type: text/plain; charset="UTF-8" Good Morning: Thanks so much for sending me a note requesting my views of NWChem which are provided below. Please refer to my Department of Chemistry/University of Connecticut web page http://rossi.chemistry.uconn.edu/ for more information about my background in High Performance Computing (HPC) and Computational Chemistry. My views are based on both experience in HPC and as an extensive use of NWChem. 1. Pre-compiled versions of NWChem I really feel that pre-compiled (static load module ) versions of NWChem should be made available. This would really enhance the popularity of NWChem over other choices. I feel that the need to compile NWChem really presents obstacles for the average user. Other computational chemistry applications provide this option (I don't like playing the comparison game.) and NWChem started out doing this. There may be a downside, but compile is always possible. NOTE: At least provide a pre-compiled serial version. When I work on a project using NWChem, I want to try multiple runs to see if the input is correct, to verify certain output, and perform overall testing. I don't like submitting my jobs to a parallel system queue at the beginning of a project. When I am sure things look good, I would switch to long-running parallel jobs. Instructions for compiling serial version and for updating an existing compiled version because of patches or personal modifications is not provided. 2. MCSCF I understand that there are other high-powered methods in NWChem for obtaining extremely accurate energies, but MCSCF provides the correct form of the wavefunction as well as static electron correlation. A good scientific paper will always include MCSCF calculations because it provides a link to chemical intuition (energies, natural orbitals, composition of orbitals). MCSCF in NWChem is weak: a) As far as I can see, it doesn't have the ability to obtain the second excited state of a given symmetry. For example, ketene, H2C=C=O ground state is ^1A_1, but one of its excited states is 2^1A_1. How do you do this with NWChem? b) I am not sure how CASSCF is implemented. c) What about state-averaged MCSCF? One should have the ability to optimize the energy average for all states under consideration, in order to compute a given excited state. d) The ability to compute a Conical Intersection is not available. This and other points described here need the ability to computed CP-MC-HF response equations. 3. Molecular Dynamics(MD) Capabilities MD needs to be updated. Please update the ability to use the CHARMM Force Field which has the best parameters for membranes. Clearly, MD in NWChem favors Amber. Why? Please broaden the MD abilities making it much easier to obtain the initial input. The format of the trajectory files is intractable making it difficult to analyze MD results with applications that use standard DCD format. Attempts at conversion did not work for me. 4. Visualization This has to be improved. There has to be a seamless interface of MWChem with visualization applications. Right now it "seems less" rather than being seamless. Other QM applications have automatic visualization capabilities: Molpro ---> Molden Orca/NAMD ---> VMD; ORCA ---> Molden; Gaussian ----> GView, Jmol/JsMol; GAMESS ---> wxmacmolplt. This is a real drawback to easy use of NWChem. Why now incorporate ECCE into NWChem. For example, when I perform a calculation, I want to visualize instantly and now go through a regime to visualize Ok. This is all I have to report now. I will write again with other comments. Warm regards, Angelo On Wed, Jun 21, 2017 at 2:08 PM, Wibe Albert de Jong nwchemex]^[gmail.com < owner-chemistry]![ccl.net> wrote: > > Sent to CCL by: "Wibe Albert de Jong" [nwchemex ~ gmail.com] > Dear users and developers, > > You are receiving this email because you are on a paper that cited the use > of the open- > source NWChem computational chemistry software. For the latest > developments of the > software suite, take a look at http://www.nwchem-sw.org . > > A US-wide team of developers, including the NWChem team at Pacific > Northwest > National Laboratory, is embarking on an ambitious effort to build a new, > modern C++ > based software, ready for a wide variety of computing platforms, including > the future > exascale supercomputers. This new code will be called NWChemEx. More about > this > effort can be found on https://www.pnnl.gov/science/ > highlights/highlight.asp?id=4411 . > > The goal of the team is to develop an open-source software suite that has > the > functionality users need, but also resolves any issues that users or > developers see with > the currently used versions of the NWChem software. Hence, we are seeking > your > feedback. > > The NWChemEx team is interesting in receiving your feedback at nwchemex(_) > gmail.com > on the major pitfalls and issues with, or positive features of NWChem, and > also the > functionality and development support you need to support your research in > the future. > > If you would like to contribute, please send us an email with your > thoughts. Your input is > crucial to ensure that NWChemEx can deliver the needs of our user > community. > > With kind regards, > > NWChem and NWChemEx software development team> > > --001a11495ff6b75ef90553f854f2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Good Morning:

Thanks= so much for sending me a note requesting my views of NWChem which are prov= ided below.=C2=A0 Please refer to my Department of Chemistry/University of = Connecticut web page

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 http://rossi.che= mistry.uconn.edu/

for more information about my background= in High Performance Computing (HPC) and Computational Chemistry.

My views are based on both experience in HPC and as an extensive use of= NWChem.=C2=A0

1. Pre-compiled versions of NWChem

I really feel that pre-compiled (static load module ) versions of N= WChem should be made available.=C2=A0 This would really enhance the popular= ity of NWChem over other choices.=C2=A0 I feel that the need to compile NWC= hem=C2=A0 really presents obstacles for the average user.=C2=A0=C2=A0 Other= computational chemistry applications provide this option (I don't like= playing the comparison game.) and NWChem started out doing this.=C2=A0 The= re may be a downside, but compile is always possible.

NOT= E:=C2=A0 At least provide a pre-compiled serial version.=C2=A0 When I work = on a project using NWChem, I want to try multiple runs to see if the input = is correct, to verify certain output, and perform overall testing.=C2=A0 I = don't like submitting my jobs to a parallel system queue at the beginni= ng of a project.=C2=A0 When I am sure things look good, I would switch to l= ong-running parallel jobs.

Instructions for compiling ser= ial version and for updating an existing compiled version because of patche= s or personal modifications is not provided.

2.=C2=A0 MCS= CF

I understand that there are other high-powered methods= in NWChem for obtaining extremely accurate energies, but MCSCF provides th= e correct form of the wavefunction as well as static electron correlation.= =C2=A0 A good scientific paper will always include MCSCF calculations becau= se it provides a link to chemical intuition (energies, natural orbitals, co= mposition of orbitals).

MCSCF in NWChem is weak:

<= /div>
a)=C2=A0 As far as I can see, it doesn't have the ability to = obtain the second excited state of a given symmetry.=C2=A0 For example, ket= ene, H2C=3DC=3DO ground state is ^1A_1, but one of its excited states is 2^= 1A_1.=C2=A0 How do you do this with NWChem?

b) I am not s= ure how CASSCF is implemented.

c)=C2=A0 What about state-= averaged MCSCF?=C2=A0 One should have the ability to optimize the energy av= erage for all states under consideration, in order to compute a given excited sta= te.

d)=C2=A0 The ability to compute a Conical Intersectio= n is not available.=C2=A0

This and other points described here need= the ability to computed CP-MC-HF response equations.

3.= =C2=A0 Molecular Dynamics(MD)=C2=A0 Capabilities

MD needs= to be updated.=C2=A0 Please update the ability to use the CHARMM Force Fie= ld which has the best parameters for membranes.=C2=A0 Clearly, MD in NWChem= favors Amber.=C2=A0 Why?=C2=A0 Please broaden the MD abilities making it m= uch easier to obtain the initial input.=C2=A0 The format of the trajectory = files is intractable making it difficult to analyze MD results with applica= tions that use standard DCD format.=C2=A0 Attempts at conversion did not wo= rk for me.

4. Visualization

This has to= be improved.=C2=A0 There has to be a seamless interface of MWChem with vis= ualization applications.=C2=A0 Right now it "seems less"=C2=A0 ra= ther than being seamless.=C2=A0 Other QM applications have automatic visual= ization capabilities:=C2=A0 Molpro ---> Molden
Orca/NAMD -= --> VMD; ORCA ---> Molden;=C2=A0 Gaussian ----> GView, Jmol/JsMol;= =C2=A0=C2=A0 GAMESS ---> wxmacmolplt.

This is a real d= rawback to easy use of NWChem.=C2=A0 Why now incorporate ECCE into NWChem.= =C2=A0 For example, when I perform a calculation, I want to visualize insta= ntly and now go through a regime to visualize

Ok.=C2=A0 T= his is all I have to report now.=C2=A0 I will write again with other commen= ts.

Warm regards,

Angelo=C2=A0



<= /div>

On Wed= , Jun 21, 2017 at 2:08 PM, Wibe Albert de Jong nwchemex]^[gmail.com <owner-chemistry]![ccl.net> wr= ote:

Sent to CCL by: "Wibe Albert de Jong" [nwchemex ~ gmail.com]
Dear users and developers,

You are receiving this email because you are on a paper that cited the use = of the open-
source NWChem computational chemistry software. For the latest developments= of the
software suite, take a look at http://www.nwchem-sw.org .

A US-wide team of developers, including the NWChem team at Pacific Northwes= t
National Laboratory, is embarking on an ambitious effort to build a new, mo= dern C++
based software, ready for a wide variety of computing platforms, including = the future
exascale supercomputers. This new code will be called NWChemEx. More about = this
effort can be found on https://www.pn= nl.gov/science/highlights/highlight.asp?id=3D4411 .

The goal of the team is to develop an open-source software suite that has t= he
functionality users need, but also resolves any issues that users or develo= pers see with
the currently used versions of the NWChem software. Hence, we are seeking y= our
feedback.

The NWChemEx team is interesting in receiving your feedback at nwchemex(_)<= a href=3D"http://gmail.com" rel=3D"noreferrer" target=3D"_blank">gmail.com<= /a>
on the major pitfalls and issues with, or positive features of NWChem, and = also the
functionality and development support you need to support your research in = the future.

If you would like to contribute, please send us an email with your thoughts= . Your input is
crucial to ensure that NWChemEx can deliver the needs of our user community= .

With kind regards,

NWChem and NWChemEx software development team



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