From owner-chemistry@ccl.net Tue Oct 18 01:44:00 2011 From: "David A Mannock dmannock[a]ualberta.ca" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45673-111018014306-19984-5X2M5ZuBT3nrvCMp8dXGxQ*server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=20cf300259c02d32e604af8c32ff Date: Mon, 17 Oct 2011 23:42:58 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock{=}ualberta.ca] --20cf300259c02d32e604af8c32ff Content-Type: text/plain; charset=ISO-8859-1 Although politics may be important in climate modeling, I thought that this was the computer chemistry forum. OK, so some chemistry happens in the atmosphere, but accurate simulations of those conditions are also important. Whether a scientist or a member of the public finds an error in such code may not be important, although it does not help when people make mistakes. Science works iteratively, through criticism from all sides. Where I see a problem politically is where people (especially those in science) have models that they have spent years working on and whose funding is dependent on those models. Not disclosing experimental protocols/computer chemistry codes maintains secrecy and it becomes more difficult to break down a poor model. I have fought this in science for 30 years and it is hard work. We are all dependent on peoples honesty and integrity, and if this info is disclosed when the manuscript is submitted for publication, bad code or unclear justification of the code can be parsed by the reviewers and clarification requested. It does not help where there is a conflict of interest between the reviewer and the authors of the MS, but that is the Editors job. It is easy to make an argument for doing nothing, governments and universities across the world have raised this response to an art form. Is this something that we should accept and be happy about? On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=}gmail.com < owner-chemistry*o*ccl.net> wrote: > For all our concerns about the impact of this manifesto on science, I think > most are missing what I believe to be an important aspect. If a code is > readily available for the scientific public, then it is readily available to > the general public. As one area mentioned in the manifesto was climate > modeling, it is clear that enterprising non-scientists or muck-raking types > can access these codes. > > In any well-commented code, there are bound to comments like "applying the > Fandoozie trick" or other such innocucous statements. In addition, in any > code of over 1000 lines there are bound to be bugs. Can you imagine the > public discourse when some rabel-rouser claims the software for climate > modeling is flawed and he shows the offending code as "proof". Flaws and > "tricks", common to all software, have the potential to be exploited for > political gain under this manifesto. > > I'm not sure where the middle ground is when trying to make software open, > accessible, and maintaining peer review without the introduction of > politics. I think this needs a lot more thought and consideration. > > Mark Zottola > --20cf300259c02d32e604af8c32ff Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Although politics may be important in climate modeling, I thought that this= was the computer chemistry forum. OK, so some chemistry happens in the atm= osphere, but accurate simulations of those conditions are also important. W= hether a scientist or a member of the public finds an error in such code ma= y not be important, although it does not help when people make mistakes. Sc= ience works iteratively, through criticism from all sides. Where I see a pr= oblem politically is where people (especially those in science) have models= that they have spent years working on and whose funding is dependent on th= ose models. Not disclosing experimental protocols/computer chemistry codes = maintains secrecy and it becomes more difficult to break down a poor model.= I have fought this in science for 30 years and it is hard work. We are all= dependent on peoples honesty and integrity, and if this info is disclosed = when the manuscript is submitted for publication, bad code or unclear justi= fication of the code can be parsed by the reviewers and clarification reque= sted. It does not help where there is a conflict of interest between the re= viewer and the authors of the MS, but that is the Editors job.

It is easy to make an argument for doing nothing, governments and unive= rsities across the world have raised this response to an art form. Is this = something that we should accept and be happy about?

On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=3D}gmail.com <owner-chemistry*o*ccl.net> wrote:
For all our concerns about the impact of this manifesto on science, I = think most are missing what I believe to be an important aspect.=A0 If a co= de is readily available for the scientific public, then it is readily avail= able to the general public.=A0 As one area mentioned in the manifesto was c= limate modeling, it is clear that enterprising non-scientists or muck-rakin= g types can access these codes.
=A0
In any well-commented code, there are bound to comments = like "applying the Fandoozie trick" or other such innocucous stat= ements.=A0 In addition, in any code of over 1000 lines there are bound to b= e bugs.=A0 Can you imagine the public discourse when some rabel-rouser clai= ms the software for climate modeling is flawed and he shows the offending c= ode as "proof".=A0 Flaws and "tricks", common to all so= ftware, have the potential to be exploited for political gain under this ma= nifesto.
=A0
I'm not sure where the middle ground is when trying = to make software open, accessible, and maintaining peer review without the = introduction of politics.=A0 I think this needs a lot more thought and cons= ideration.

Mark Zottola

--20cf300259c02d32e604af8c32ff-- From owner-chemistry@ccl.net Tue Oct 18 02:37:00 2011 From: "Rzepa Henry h.rzepa_-_imperial.ac.uk" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45674-111018023127-8024-STdvdGzwO2XglisF9/FbVA~~server.ccl.net> X-Original-From: Rzepa Henry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 18 Oct 2011 07:31:16 +0100 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Rzepa Henry [h.rzepa]~[imperial.ac.uk] On 17 Oct 2011, at 21:41, Brian Salter-Duke brian.james.duke|,|gmail.com wrote: > > Sent to CCL by: Brian Salter-Duke [brian.james.duke^_^gmail.com] > Just using a different code leads to confusion. Code A gives X. Code B > gives Y, But why? A known example of this confusion is the differing > meanings of B3LYP in different programs, but what if the reason is not > clear. > > Also, what if it is an entirely new development that is not in any > other program. Of course I assume the paper explains the method and > someone else could code it up, but that is time consuming. It would be > much preferable to check the code that gave the results. > > However, I am a total open source supporter and nothing is going to > convince me that keeping scientific code closed to the users of the > program is anything other than bad science and really rather > offensive. Science does not progress by secrecy. > I strongly welcome the principles espoused. I recollect about 22 years ago a student of mine struggling to reproduce published numbers using a specified code. After about 3 months of effort he got close (but not exactly), by "reverse engineering" various program defaults that had changed from the version used to publish the results and the version we were using ourselves. Needless to say, the code was "closed". If you want another example of how code changes can change things, you only have to look at solvation codes and properties such as chiroptical spectra. From owner-chemistry@ccl.net Tue Oct 18 05:33:00 2011 From: "Joaquin Calbo HimPhoenixCCL- -gmail.com" To: CCL Subject: CCL: NWChem Running in Parallel Message-Id: <-45675-111018053150-21819-DmSm2DmFg8L7/pIyDkxTOg .. server.ccl.net> X-Original-From: "Joaquin Calbo" Date: Tue, 18 Oct 2011 05:31:47 -0400 Sent to CCL by: "Joaquin Calbo" [HimPhoenixCCL---gmail.com] Hello everybody, I'm very interested in running NWChem in parallel. However an error occurs when try to do that type of jobs (single processor jobs run correclty). As I've read I put in my shuttle the next command: /soft/nwchem_6_0/bin/parallel /soft/newchem_6_0/bin/nwchem $PBS_O_WORKDIR/$name.nw >& $PBS_O_WORKDIR/$name.out in addition to the line #PBS -l nodes=MACHINE:ppn=8 The error it sends back to me in the .out file is: Master: PROCGRP = PROCGRP tmp = /home/USER/pdir//soft/newchem_6_0/bin/nwchem.p 0: Master: failed to open PROCGRP 0 (0). 0: Master: failed to open PROCGRP 0 (0). system error message: No such file or directory Must I include some extra information in the .nw input file about the number of processors to use or define an environmental variable? Or is it an external problem of the software compilation? Any suggestion would be really appreciate, Thanks in advance. Joaquin From owner-chemistry@ccl.net Tue Oct 18 07:08:00 2011 From: "psavita psavita*crlindia.com" To: CCL Subject: CCL: NWChem Running in Parallel Message-Id: <-45676-111018062522-7579-GIUFxPzVElk9vJOiHA7k+w^-^server.ccl.net> X-Original-From: psavita Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 18 Oct 2011 15:54:57 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita [psavita- -crlindia.com]
Hello,

I am not familiar with the PBS system, we use LS= F.
However, often the problem is with the availability of
.nwchemrc f= ile in the $HOME folder that specifies
paths to different force field a= nd basis set libraries.
The INSTALL instructions include contents of the= file.

Best luck,

= Savita Pundlik
Computational Materials Applied Research Group
Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road<= span style=3D"font-style: italic; font-family: Georgia,Default Serif,serif;= ">Pune - 411004, India.<= br>


-----owner-= chemistry+psavita=3D=3Dcrlindia.com,+,ccl.net wrote: -----

To: "Pundlik, Savita Sun= il " <psavita,+,crlindia.com>
From: "Joaquin Calbo HimPhoen= ixCCL- -gmail.com" <owner-chemistry,+,ccl.net>
Sent by: owner-chemistry+psavita=3D=3Dcrlindia.com,+,ccl.net<= br>Date: 10/18/2011 03:01PM
Subject: CCL: NWChem Running in Parallel
=

Sent to CCL= by: "Joaquin  Calbo" [HimPhoenixCCL---gmail.com]
Hello everybody,<= br>
I'm very interested in running NWChem in parallel. However an error = occurs when try to do that type of jobs (single processor jobs run correclt= y). As I've read I put in my shuttle the next command:

/soft/nwchem= =5F6=5F0/bin/parallel /soft/newchem=5F6=5F0/bin/nwchem $PBS=5FO=5FWORKDIR/$= name.nw >& $PBS=5FO=5FWORKDIR/$name.out

in addition to the li= ne #PBS -l nodes=3DMACHINE:ppn=3D8

The error it sends back to me in = the .out file is:

Master: PROCGRP =3D PROCGRP
tmp =3D /home/USER/= pdir//soft/newchem=5F6=5F0/bin/nwchem.p
0: Master: failed to open PROCGR= P 0 (0).
0: Master: failed to open PROCGRP 0 (0).
system error messag= e: No such file or directory

Must I include some extra information i= n the .nw input file about the number of processors to use or define an env= ironmental variable? Or is it an external problem of the software compilati= on?

Any suggestion would be really appreciate,
Thanks in advance.=

Joaquin



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=0D<= br>
=0D--------------------------------------------------------= -----------------------=0DSupercomputing 2011 (SC11)=0DSeattle, WA, USA, No= vember 14 - 18, 2011=0DVisit CRL at Booth #4505, Level 6=0D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
= From owner-chemistry@ccl.net Tue Oct 18 09:19:00 2011 From: "Mark Zottola mzottola ~ gmail.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45677-111018085152-13544-62hDGY6kIznRvaDUYM23/g===server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=bcaec5215d7b64127d04af922f25 Date: Tue, 18 Oct 2011 08:51:41 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola---gmail.com] --bcaec5215d7b64127d04af922f25 Content-Type: text/plain; charset=ISO-8859-1 "Although politics may be important in climate modeling, I thought that this was the computer chemistry forum." Monte Python once did a skit that you never know when the Spanish Inquisition will show up. I used weather modeling as an example, but the bigger point is that who knows what ox is next to be gored. Computational chemistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the next battleground the luddites in the US would latch on to. Or There seems to be a yin and a yang to this idea. Full disclosure of everything to anyone sounds good. But there are business concerns to be addressed - can you imagine Gaussian putting their code in for full public scrutiny? Government scientists using home grown codes face publication issues due to overzealous Public Affairs Officers or their superiors refusing to release codes in the vague name of national security. Similarly, in closed systems like China who may refuse publication of their internally developed codes, would we lose significant knowledge because we refused to accept their papers due to this "manifesto"? Finally, the specter of Mencken's booboise misusing that access to information. On the other hand, the QCPE was a great idea, but it seems to have died in the academic rush to make money. Having codes readily available for dissemination and use would be a positive for the community. Total non disclosure, copyrighting and hiding codes does seem to protect the economic interests of those who have excelled in making money off their codes. It sanctifies the current economic model used for making money in computational chemistry. While there are benefits to this mixture of economics and secrecy, the question is whether this is consistent with the goals of science. The current two-tiered system in place - some software available for public scrutiny, others protected as though it were the secret to the universe probably does need some tweaking. But it is hard to see how a far-ranging manifesto like this is going to solve much considering the utter disruption its full implementation would cause. On Tue, Oct 18, 2011 at 1:42 AM, David A Mannock dmannock[a]ualberta.ca < owner-chemistry(a)ccl.net> wrote: > Although politics may be important in climate modeling, I thought that this > was the computer chemistry forum. OK, so some chemistry happens in the > atmosphere, but accurate simulations of those conditions are also important. > Whether a scientist or a member of the public finds an error in such code > may not be important, although it does not help when people make mistakes. > Science works iteratively, through criticism from all sides. Where I see a > problem politically is where people (especially those in science) have > models that they have spent years working on and whose funding is dependent > on those models. Not disclosing experimental protocols/computer chemistry > codes maintains secrecy and it becomes more difficult to break down a poor > model. I have fought this in science for 30 years and it is hard work. We > are all dependent on peoples honesty and integrity, and if this info is > disclosed when the manuscript is submitted for publication, bad code or > unclear justification of the code can be parsed by the reviewers and > clarification requested. It does not help where there is a conflict of > interest between the reviewer and the authors of the MS, but that is the > Editors job. > > It is easy to make an argument for doing nothing, governments and > universities across the world have raised this response to an art form. Is > this something that we should accept and be happy about? > > > On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=}gmail.com < > owner-chemistry*ccl.net> wrote: > >> For all our concerns about the impact of this manifesto on science, I >> think most are missing what I believe to be an important aspect. If a code >> is readily available for the scientific public, then it is readily available >> to the general public. As one area mentioned in the manifesto was climate >> modeling, it is clear that enterprising non-scientists or muck-raking types >> can access these codes. >> >> In any well-commented code, there are bound to comments like "applying the >> Fandoozie trick" or other such innocucous statements. In addition, in any >> code of over 1000 lines there are bound to be bugs. Can you imagine the >> public discourse when some rabel-rouser claims the software for climate >> modeling is flawed and he shows the offending code as "proof". Flaws and >> "tricks", common to all software, have the potential to be exploited for >> political gain under this manifesto. >> >> I'm not sure where the middle ground is when trying to make software open, >> accessible, and maintaining peer review without the introduction of >> politics. I think this needs a lot more thought and consideration. >> >> Mark Zottola >> > > --bcaec5215d7b64127d04af922f25 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
"Although politics may be important in climate modeling, I though= t that this was the computer chemistry forum."
=A0
Monte Python once did a skit that you never know when the Spanish Inquisit= ion will show up.=A0 I used weather modeling as an example, but the bigger = point is that who knows what ox is next to be gored.=A0=A0Computational che= mistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the nex= t battleground the=A0luddites in the US would latch on to.=A0 Or =A0
=A0
There seems to be a yin and a yang to this idea.=A0 Full= disclosure of everything to anyone sounds good.=A0 But there are business = concerns to be addressed - can you imagine Gaussian putting their code in f= or full public scrutiny?=A0 Government scientists using home grown codes fa= ce publication issues due to overzealous Public Affairs Officers or their s= uperiors refusing to release codes in the vague name of national security.= =A0 Similarly, in closed systems like China who may refuse publication of t= heir internally developed codes, would we lose significant knowledge becaus= e we refused to accept their papers due to this "manifesto"?=A0 F= inally, the specter of Mencken's booboise misusing that access to infor= mation.
=A0
On the other hand, the QCPE was a great idea, but it see= ms to have died in the academic rush to make money.=A0 Having codes readily= available for dissemination and use would be a positive for the community.=
=A0
Total non disclosure, copyrighting and hiding codes does= seem to protect the economic interests of those who have excelled in makin= g money off their codes.=A0 It sanctifies the current economic model used f= or making money in computational chemistry.=A0 While there are benefits to = this mixture of economics and secrecy, the question is whether this is cons= istent with the goals of science.=A0
=A0
The current two-tiered system in place - some software a= vailable for public scrutiny, others protected as though it were the secret= to the universe probably does need some tweaking.=A0 But it is hard to see= how a far-ranging manifesto like this is going to solve much considering t= he utter disruption its full implementation would cause.

On Tue, Oct 18, 2011 at 1:42 AM, David= A Mannock dmannock[a]ualberta.ca <owner-chemistry(a)= ccl.net> wrote:
Although politics may be important in climate = modeling, I thought that this was the computer chemistry forum. OK, so some= chemistry happens in the atmosphere, but accurate simulations of those con= ditions are also important. Whether a scientist or a member of the public f= inds an error in such code may not be important, although it does not help = when people make mistakes. Science works iteratively, through criticism fro= m all sides. Where I see a problem politically is where people (especially = those in science) have models that they have spent years working on and who= se funding is dependent on those models. Not disclosing experimental protoc= ols/computer chemistry codes maintains secrecy and it becomes more difficul= t to break down a poor model. I have fought this in science for 30 years an= d it is hard work. We are all dependent on peoples honesty and integrity, a= nd if this info is disclosed when the manuscript is submitted for publicati= on, bad code or unclear justification of the code can be parsed by the revi= ewers and clarification requested. It does not help where there is a confli= ct of interest between the reviewer and the authors of the MS, but that is = the Editors job.

It is easy to make an argument for doing nothing, governments and unive= rsities across the world have raised this response to an art form. Is this = something that we should accept and be happy about?


On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=3D}gmail.com <owner-chemistry*ccl.n= et> wrote:
For all our concerns about the impact of this manifesto on science, I = think most are missing what I believe to be an important aspect.=A0 If a co= de is readily available for the scientific public, then it is readily avail= able to the general public.=A0 As one area mentioned in the manifesto was c= limate modeling, it is clear that enterprising non-scientists or muck-rakin= g types can access these codes.
=A0
In any well-commented code, there are bound to comments = like "applying the Fandoozie trick" or other such innocucous stat= ements.=A0 In addition, in any code of over 1000 lines there are bound to b= e bugs.=A0 Can you imagine the public discourse when some rabel-rouser clai= ms the software for climate modeling is flawed and he shows the offending c= ode as "proof".=A0 Flaws and "tricks", common to all so= ftware, have the potential to be exploited for political gain under this ma= nifesto.
=A0
I'm not sure where the middle ground is when trying = to make software open, accessible, and maintaining peer review without the = introduction of politics.=A0 I think this needs a lot more thought and cons= ideration.

Mark Zottola


--bcaec5215d7b64127d04af922f25-- From owner-chemistry@ccl.net Tue Oct 18 11:51:00 2011 From: "Jim Kress ccl_nospam*o*kressworks.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45678-111018115007-24383-iHI0HYKTODdV/qMgqQjOJA|,|server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0034_01CC8D8C.0DBC3DC0" Date: Tue, 18 Oct 2011 11:49:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam,kressworks.com] This is a multipart message in MIME format. ------=_NextPart_000_0034_01CC8D8C.0DBC3DC0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Oh yeah. We can't let the great unwashed masses view our code. They are so dumb. We might be embarrassed. /sarcasm That kind of elitist attitude is why many people have lost faith in the Science that is being promulgated today. Elitism has no place in Science. We are supposed to be professionals, not oracles. If you are ashamed of the whimsy you place in the comments in the code, then don't put it there. Perhaps exposure to the public will lead to more professionalism in what we produce. Jim Kress > From: owner-chemistry+ccl_nospam==kressworks.com|-|ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com|-|ccl.net] On Behalf Of Mark Zottola mzottola{=}gmail.com Sent: Monday, October 17, 2011 9:09 PM To: Kress, Jim Subject: CCL: Science code manifesto For all our concerns about the impact of this manifesto on science, I think most are missing what I believe to be an important aspect. If a code is readily available for the scientific public, then it is readily available to the general public. As one area mentioned in the manifesto was climate modeling, it is clear that enterprising non-scientists or muck-raking types can access these codes. In any well-commented code, there are bound to comments like "applying the Fandoozie trick" or other such innocucous statements. In addition, in any code of over 1000 lines there are bound to be bugs. Can you imagine the public discourse when some rabel-rouser claims the software for climate modeling is flawed and he shows the offending code as "proof". Flaws and "tricks", common to all software, have the potential to be exploited for political gain under this manifesto. I'm not sure where the middle ground is when trying to make software open, accessible, and maintaining peer review without the introduction of politics. I think this needs a lot more thought and consideration. Mark Zottola ------=_NextPart_000_0034_01CC8D8C.0DBC3DC0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Oh = yeah.  We can’t let the great unwashed masses view our = code.  They are so dumb.  We might be embarrassed.  = /sarcasm

 

That kind of elitist attitude is why many people have = lost faith in the Science that is being promulgated today.  Elitism = has no place in Science.  We are supposed to be professionals, not = oracles.

 

If you are ashamed of the whimsy you place in the = comments in the code, then don’t put it there.  Perhaps = exposure to the public will lead to more professionalism in what we = produce.

 

Jim Kress

 

 

From:= = owner-chemistry+ccl_nospam=3D=3Dkressworks.com|-|ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com|-|ccl.net] On = Behalf Of Mark Zottola mzottola{=3D}gmail.com
Sent: = Monday, October 17, 2011 9:09 PM
To: Kress, Jim =
Subject: CCL: Science code = manifesto

 

For all = our concerns about the impact of this manifesto on science, I think most = are missing what I believe to be an important aspect.  If a code is = readily available for the scientific public, then it is readily = available to the general public.  As one area mentioned in the = manifesto was climate modeling, it is clear that enterprising = non-scientists or muck-raking types can access these = codes.

 

In any well-commented code, there are bound to = comments like "applying the Fandoozie trick" or other such = innocucous statements.  In addition, in any code of over 1000 lines = there are bound to be bugs.  Can you imagine the public discourse = when some rabel-rouser claims the software for climate modeling is = flawed and he shows the offending code as "proof".  Flaws = and "tricks", common to all software, have the potential to be = exploited for political gain under this = manifesto.

 

I'm not sure where the middle ground is = when trying to make software open, accessible, and maintaining peer = review without the introduction of politics.  I think this needs a = lot more thought and consideration.

Mark = Zottola

------=_NextPart_000_0034_01CC8D8C.0DBC3DC0-- From owner-chemistry@ccl.net Tue Oct 18 12:49:00 2011 From: "N. Sukumar nagams(!)rpi.edu" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45679-111018115633-3430-3UE551MwkRUeIjB+TLQleQ~~server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Tue, 18 Oct 2011 11:57:09 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams**rpi.edu] Economic and national security concerns could be legitimate issues, but hiding science from the public (who pays for it) in order to protect it > from luddites or from political attacks is the most ridiculous thing I've heard yet. They used to do something like that in the Dark Ages, hiding whatever science there was behind magic spells, rites of initiation and oaths of secrecy - and we know how well science flourished during those times. They were called the Dark Ages for a reason! At best such tactics will be counter-productive and discredit such secret scientific results. It would then truly be a case of My (Holy) Book versus Your Book! As I read it, the manifesto only applies to results meant for publication. Since classified defense research does not generally make it into publication, the issue would therefore be moot with regard to genuine national security concerns. And yes, I can imagine Gaussian making their code available for public scrutiny. In fact, they do so now; many scientists around the world have access to and are able to scrutinize the source code, or even modify it for their private use. Their restrictions concern reproduction (copyright), redistribution, re-engineering and publication of benchmarks related to performance, not whether there are bugs in the algorithm or not. It was also mentioned in this discussion that journal editors/reviewers do not have the time or resources to verify source code or reproduce results and that you cannot expect a research group to shut down their lab while you try to reproduce their results on their systems. By and large this is generally true, but in cases of exceptional interest/importance (e.g. the case of homeopathy), Nature for instance has been known to send out a team of editors/reviewers to do just that. However, it is unrealistic to expect unpaid reviewers to bear the full responsibility for fact-checking all the intricate details of the code used to generate scientific results. On the whole, this works best by the self-correcting, re-engineering, crowd-sourcing nature of the scientific enterprise, but having the raw data and source code available for inspection in those exceptional circumstances (as in the example above or as in the case of anthropocentric global warming) is important for ensuring transparency and confidence in the scientific results. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "A Drug is any substance which, when injected into a rat, produces a publishable, scientific paper." ==============Original message text=============== On Tue, 18 Oct 2011 8:51:41 EDT "Mark Zottola mzottola ~ gmail.com" wrote: "Although politics may be important in climate modeling, I thought that this was the computer chemistry forum." Monte Python once did a skit that you never know when the Spanish Inquisition will show up. I used weather modeling as an example, but the bigger point is that who knows what ox is next to be gored. Computational chemistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the next battleground the luddites in the US would latch on to. Or There seems to be a yin and a yang to this idea. Full disclosure of everything to anyone sounds good. But there are business concerns to be addressed - can you imagine Gaussian putting their code in for full public scrutiny? Government scientists using home grown codes face publication issues due to overzealous Public Affairs Officers or their superiors refusing to release codes in the vague name of national security. Similarly, in closed systems like China who may refuse publication of their internally developed codes, would we lose significant knowledge because we refused to accept their papers due to this "manifesto"? Finally, the specter of Mencken's booboise misusing that access to information. On the other hand, the QCPE was a great idea, but it seems to have died in the academic rush to make money. Having codes readily available for dissemination and use would be a positive for the community. Total non disclosure, copyrighting and hiding codes does seem to protect the economic interests of those who have excelled in making money off their codes. It sanctifies the current economic model used for making money in computational chemistry. While there are benefits to this mixture of economics and secrecy, the question is whether this is consistent with the goals of science. The current two-tiered system in place - some software available for public scrutiny, others protected as though it were the secret to the universe probably does need some tweaking. But it is hard to see how a far-ranging manifesto like this is going to solve much considering the utter disruption its full implementation would cause. On Tue, Oct 18, 2011 at 1:42 AM, David A Mannock dmannock[a]ualberta.ca < owner-chemistry###ccl.net> wrote: > Although politics may be important in climate modeling, I thought that this > was the computer chemistry forum. OK, so some chemistry happens in the > atmosphere, but accurate simulations of those conditions are also important. > Whether a scientist or a member of the public finds an error in such code > may not be important, although it does not help when people make mistakes. > Science works iteratively, through criticism from all sides. Where I see a > problem politically is where people (especially those in science) have > models that they have spent years working on and whose funding is dependent > on those models. Not disclosing experimental protocols/computer chemistry > codes maintains secrecy and it becomes more difficult to break down a poor > model. I have fought this in science for 30 years and it is hard work. We > are all dependent on peoples honesty and integrity, and if this info is > disclosed when the manuscript is submitted for publication, bad code or > unclear justification of the code can be parsed by the reviewers and > clarification requested. It does not help where there is a conflict of > interest between the reviewer and the authors of the MS, but that is the > Editors job. > > It is easy to make an argument for doing nothing, governments and > universities across the world have raised this response to an art form. Is > this something that we should accept and be happy about? > > > On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=}gmail.com < > owner-chemistry*ccl.net> wrote: > >> For all our concerns about the impact of this manifesto on science, I >> think most are missing what I believe to be an important aspect. If a code >> is readily available for the scientific public, then it is readily available >> to the general public. As one area mentioned in the manifesto was climate >> modeling, it is clear that enterprising non-scientists or muck-raking types >> can access these codes. >> >> In any well-commented code, there are bound to comments like "applying the >> Fandoozie trick" or other such innocucous statements. In addition, in any >> code of over 1000 lines there are bound to be bugs. Can you imagine the >> public discourse when some rabel-rouser claims the software for climate >> modeling is flawed and he shows the offending code as "proof". Flaws and >> "tricks", common to all software, have the potential to be exploited for >> political gain under this manifesto. >> >> I'm not sure where the middle ground is when trying to make software open, >> accessible, and maintaining peer review without the introduction of >> politics. I think this needs a lot more thought and consideration. >> >> Mark Zottola >> > > ===========End of original message text=========== From owner-chemistry@ccl.net Tue Oct 18 13:44:00 2011 From: "Robert Perkins cclnanolab(!)gmail.com" To: CCL Subject: CCL: MO overlap CASSCF Message-Id: <-45680-111018134024-1891-nsoB1ZKJYpcdSYSVns4vlQ]-[server.ccl.net> X-Original-From: Robert Perkins Content-Type: multipart/alternative; boundary=001517475eb6d804be04af9635f6 Date: Tue, 18 Oct 2011 19:39:50 +0200 MIME-Version: 1.0 Sent to CCL by: Robert Perkins [cclnanolab ~ gmail.com] --001517475eb6d804be04af9635f6 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I would like to calculate overlap integral of two orbitals in CAS calculations. Do you know how to do that in G09? Best regards R.P. --001517475eb6d804be04af9635f6 Content-Type: text/html; charset=ISO-8859-1 Dear All,
I would like to calculate overlap integral of two orbitals in CAS calculations. Do you know how to do that in G09?
Best regards
R.P.
--001517475eb6d804be04af9635f6-- From owner-chemistry@ccl.net Tue Oct 18 14:18:00 2011 From: "Mark Zottola mzottola . gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45681-111018134721-6925-qpCFFO4+pPwQSr7c/eeRQg|server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=bcaec520f1cf31208d04af9650eb Date: Tue, 18 Oct 2011 13:47:12 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola##gmail.com] --bcaec520f1cf31208d04af9650eb Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Jim, The fact that an email mentioning a statistical "trick" for analyzing the climate data caused a brouhaha was inane. As a scientist, i have no proble= m saying a trick - beit computational or experimental - solved a problem because no one in a scientific audience would interpret that word to mean anything other than some slight cleverness to achieve a goal. To the Luddites, a trick is a lie and therefore the scientists are using lies. It is not elitist in this atmosphere to be concerned about what people who deliberately twist words will do with comments in the code. The fact is that we live in an anti-scientific world where the severe exercise of reaso= n (i.e. science) is displaced by gut feelings and other idiotic nonsequitirs by the obscuratum. As far as professionalism goes, as long as the code produces scientifically valid results, the content of comments should not b= e a concern to anyone. On Tue, Oct 18, 2011 at 11:49 AM, Jim Kress ccl_nospam*o*kressworks.com < owner-chemistry]![ccl.net> wrote: > Oh yeah. We can=92t let the great unwashed masses view our code. They = are > so dumb. We might be embarrassed. /sarcasm**** > > ** ** > > That kind of elitist attitude is why many people have lost faith in the > Science that is being promulgated today. Elitism has no place in Science= . > We are supposed to be professionals, not oracles.**** > > ** ** > > If you are ashamed of the whimsy you place in the comments in the code, > then don=92t put it there. Perhaps exposure to the public will lead to m= ore > professionalism in what we produce.**** > > ** ** > > Jim Kress**** > > ** ** > > ** ** > > *From:* owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net [mailto: > owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net] *On Behalf Of *= Mark > Zottola mzottola{=3D}gmail.com > *Sent:* Monday, October 17, 2011 9:09 PM > *To:* Kress, Jim > *Subject:* CCL: Science code manifesto**** > > ** ** > > For all our concerns about the impact of this manifesto on science, I thi= nk > most are missing what I believe to be an important aspect. If a code is > readily available for the scientific public, then it is readily available= to > the general public. As one area mentioned in the manifesto was climate > modeling, it is clear that enterprising non-scientists or muck-raking typ= es > can access these codes.**** > > **** > > In any well-commented code, there are bound to comments like "applying th= e > Fandoozie trick" or other such innocucous statements. In addition, in an= y > code of over 1000 lines there are bound to be bugs. Can you imagine the > public discourse when some rabel-rouser claims the software for climate > modeling is flawed and he shows the offending code as "proof". Flaws and > "tricks", common to all software, have the potential to be exploited for > political gain under this manifesto.**** > > **** > > I'm not sure where the middle ground is when trying to make software open= , > accessible, and maintaining peer review without the introduction of > politics. I think this needs a lot more thought and consideration.**** > > Mark Zottola**** > --bcaec520f1cf31208d04af9650eb Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Jim,
=A0
The fact that an email mentioning a statistical "trick" for = analyzing the climate data caused a brouhaha was inane.=A0 As a scientist, = i have no problem saying a trick - beit computational or experimental - sol= ved a problem because no one in a scientific audience would interpret that = word to mean anything other than some slight cleverness to achieve a goal.= =A0 To the Luddites, a=A0trick is a lie and therefore the scientists are us= ing lies.=A0
=A0
It is not elitist in this atmosphere to be concerned about what peop= le who deliberately twist words will do with comments in the code.=A0 The f= act is that we live in an anti-scientific world where the severe exercise o= f reason (i.e. science) is displaced by gut feelings and other idiotic nons= equitirs by the obscuratum.=A0 As far as professionalism goes, as long as t= he code produces scientifically valid results, the content of comments shou= ld not be a concern to anyone.

On Tue, Oct 18, 2011 at 11:49 AM, Jim Kress ccl_= nospam*o*kressworks.com <owner-chemistry]![ccl.net= > wrote:

Oh yeah.=A0 We can=92t let the great unwashed masses= view our code.=A0 They are so dumb.=A0 We might be embarrassed.=A0 /sarcas= m

=A0

That kind of elitist attitude is why many people hav= e lost faith in the Science that is being promulgated today.=A0 Elitism has= no place in Science.=A0 We are supposed to be professionals, not oracles.<= u>

=A0

If you are ashamed of the whimsy you place in the co= mments in the code, then don=92t put it there.=A0 Perhaps exposure to the p= ublic will lead to more professionalism in what we produce.

=A0

Jim Kress

<= /u>=A0

<= /u>=A0

From:<= span style=3D"FONT-SIZE: 10pt"> owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net [mailto:owner-chemistry+ccl_nospam= =3D=3Dkressworks.com(a)ccl.net] On Behal= f Of Mark Zottola mzottola{=3D}gmail.com
Sent: Monday, October 17, 2011 9:09 PM
To: Kress, Jim
= Subject: CCL: Science code manifesto

<= /div>

=A0

For all our concerns about the impact of this manife= sto on science, I think most are missing what I believe to be an important = aspect.=A0 If a code is readily available for the scientific public, then i= t is readily available to the general public.=A0 As one area mentioned in t= he manifesto was climate modeling, it is clear that enterprising non-scient= ists or muck-raking types can access these codes.

=A0

In any well-commented code, there are bound to comme= nts like "applying the Fandoozie trick" or other such innocucous = statements.=A0 In addition, in any code of over 1000 lines there are bound = to be bugs.=A0 Can you imagine the public discourse when some rabel-rouser = claims the software for climate modeling is flawed and he shows the offendi= ng code as "proof".=A0 Flaws and "tricks", common to al= l software, have the potential to be exploited for political gain under thi= s manifesto.

=A0

I'm not sure where= the middle ground is when trying to make software open, accessible, and ma= intaining peer review without the introduction of politics.=A0 I think this= needs a lot more thought and consideration.

Mark Zottola


--bcaec520f1cf31208d04af9650eb-- From owner-chemistry@ccl.net Tue Oct 18 14:53:00 2011 From: "Alcides Simao alsimao _ gmail.com" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45682-111018134233-2945-1395kTmPino6/RGYr0lDVg(!)server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=0015174c3654d28b5c04af963d09 Date: Tue, 18 Oct 2011 18:42:03 +0100 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao**gmail.com] --0015174c3654d28b5c04af963d09 Content-Type: text/plain; charset=ISO-8859-1 Hello all! The first time I saw Brian posting the very first e-mail about this, I had to laugh. Why? Because I knew that this 'philosophical' mail would endure much past any mail regarding any known molecule to mankind. I see a lot of dispersed opinions. Some say that the code should be free. Others, that it should be commercial. Some say that the methods are explained. Some don't say nothing. Others say it all. and so on... Well... I thought a bit about this and I came up with a laughable idea that may actually work. It won't be as open as one would like, however, it would give a very good insight on how the programs work. The system is based on the following premises: a) Nor Physics nor mathematics can not be 'patented', hence all mathematical engineering used in a program must be accessible and peer-reviewed b) Programs are based on subroutines - one would suffice to know how the subroutine works - the code itself doesn't matter c) a decision tree that describes how the program works for each and every soubroutine, describing all the math done step by step, and intelocking it with the program's calculation 'run' . It may indeed be laughable, maybe childish, but let us remind of something. Commercial programs are built by programmers (mostly!). Programmers have a different toolkit that a chemist have. So, programing styles exist, however it is not the programming style that we are after, but the way the program itself works. Some companies will, obviously, defend their interests by stating that the code is subjected to copyright. But you can't copyright mathematics and physics. So, for a full revision of the code, I believe that a decision tree would suffice to understand what is being done. It's a way to go around the copyright problem. It's like having a map of the program instead of the program itself. for instance, if someone uses Krylov's subspaces to decompose a matrix, instead of Gauss-Siedel's, it may speed up a calculation in a extreme fashion! that fact allows to understand, for instance, what is the reason behind a delay in the calculation. I believe that, in the spirit of fairness, this information is the LEAST and, sincerely, less doubtful way to understand how a program works. Of course that a lot of road must be covered, but I believe that this is a good way to lead us to the right spot. Thank you for the time you spent for reading the email posted by a guy with a running nose! Goddam weather! Best, Al --0015174c3654d28b5c04af963d09 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello all!

The first time I saw Brian posting the very first e-mail = about this, I had to laugh. Why? Because I knew that this 'philosophica= l' mail would endure much past any mail regarding any known molecule to= mankind.

I see a lot of dispersed opinions. Some say that the code should be fre= e. Others, that it should be commercial. Some say that the methods are expl= ained. Some don't say nothing. Others say it all. and so on...

Well... I thought a bit about this and I came up with a laughable idea that= may actually work. It won't be as open as one would like, however, it = would give a very good insight on how the programs work.

The system = is based on the following premises:

a) Nor Physics nor mathematics can not be 'patented', hence all= mathematical engineering used in a program must be accessible and peer-rev= iewed
b) Programs are based on subroutines - one would suffice to know h= ow the subroutine works - the code itself doesn't matter
c) a decision tree that describes how the program works for each and every = soubroutine, describing all the math done step by step, and intelocking it = with the program's calculation 'run' .

It may indeed be = laughable, maybe childish, but let us remind of something. Commercial progr= ams are built by programmers (mostly!). Programmers have a different toolki= t that a chemist have. So, programing styles exist, however it is not the p= rogramming style that we are after, but the way the program itself works.
Some companies will, obviously, defend their interests by stating that = the code is subjected to copyright. But you can't copyright mathematics= and physics. So, for a full revision of the code, I believe that a decisio= n tree would suffice to understand what is being done. It's a way to go= around the copyright problem. It's like having a map of the program in= stead of the program itself.

for instance, if someone uses Krylov's subspaces to decompose a mat= rix, instead of Gauss-Siedel's, it may speed up a calculation in a extr= eme fashion! that fact allows to understand, for instance, what is the reas= on behind a delay in the calculation.

I believe that, in the spirit of fairness, this information is the LEAS= T and, sincerely, less doubtful way to understand how a program works. Of c= ourse that a lot of road must be covered, but I believe that this is a good= way to lead us to the right spot.

Thank you for the time you spent for reading the email posted by a guy = with a running nose! Goddam weather!

Best,

Al


--0015174c3654d28b5c04af963d09-- From owner-chemistry@ccl.net Tue Oct 18 15:28:00 2011 From: "Vincent Leroux vincent.leroux- -loria.fr" To: CCL Subject: CCL: Science code manifesto - just publish the code Message-Id: <-45683-111018143305-2177-USMS+DicAa0E5Kj6fYoaUg(-)server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Oct 2011 20:32:47 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux..loria.fr] I do not understand how this could lead to such a heated debate. Wherever access to the code is necessary to reproduce results, it *must* be provided one way or another (e.g. as supporting information) if it is not freely available already, this is just plain obvious to me. Wondering why a manifesto would be needed in order to do just that... But it looks like some consider their code as a part of themselves, or are afraid of the potential criticisms, for we scientists do not have a reputation of coding "cleanly"... Well... everything was said here already: http://www.nature.com/news/2010/101013/full/467753a.html Regards VL From owner-chemistry@ccl.net Tue Oct 18 16:03:00 2011 From: "David A Mannock dmannock:_:ualberta.ca" To: CCL Subject: CCL: Science code manifesto Message-Id: <-45684-111018144843-18054-t5bixxkhwEOxsyX1SSGvJg^-^server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=0022158df36fc9b84c04af972bb9 Date: Tue, 18 Oct 2011 12:48:36 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock]=[ualberta.ca] --0022158df36fc9b84c04af972bb9 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Excuse me? Is this the 10 minute argument or the full half hour? On Tue, Oct 18, 2011 at 11:47 AM, Mark Zottola mzottola . gmail.com < owner-chemistry+/-ccl.net> wrote: > Jim, > > The fact that an email mentioning a statistical "trick" for analyzing the > climate data caused a brouhaha was inane. As a scientist, i have no prob= lem > saying a trick - beit computational or experimental - solved a problem > because no one in a scientific audience would interpret that word to mean > anything other than some slight cleverness to achieve a goal. To the > Luddites, a trick is a lie and therefore the scientists are using lies. > > It is not elitist in this atmosphere to be concerned about what people wh= o > deliberately twist words will do with comments in the code. The fact is > that we live in an anti-scientific world where the severe exercise of rea= son > (i.e. science) is displaced by gut feelings and other idiotic nonsequitir= s > by the obscuratum. As far as professionalism goes, as long as the code > produces scientifically valid results, the content of comments should not= be > a concern to anyone. > > On Tue, Oct 18, 2011 at 11:49 AM, Jim Kress ccl_nospam*o*kressworks.com < > owner-chemistry-.-ccl.net> wrote: > >> Oh yeah. We can=92t let the great unwashed masses view our code. They >> are so dumb. We might be embarrassed. /sarcasm**** >> >> ** ** >> >> That kind of elitist attitude is why many people have lost faith in the >> Science that is being promulgated today. Elitism has no place in Scienc= e. >> We are supposed to be professionals, not oracles.**** >> >> ** ** >> >> If you are ashamed of the whimsy you place in the comments in the code, >> then don=92t put it there. Perhaps exposure to the public will lead to = more >> professionalism in what we produce.**** >> >> ** ** >> >> Jim Kress**** >> >> ** ** >> >> ** ** >> >> *From:* owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net [mailto= : >> owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net] *On Behalf Of = *Mark >> Zottola mzottola{=3D}gmail.com >> *Sent:* Monday, October 17, 2011 9:09 PM >> *To:* Kress, Jim >> *Subject:* CCL: Science code manifesto**** >> >> ** ** >> >> For all our concerns about the impact of this manifesto on science, I >> think most are missing what I believe to be an important aspect. If a c= ode >> is readily available for the scientific public, then it is readily avail= able >> to the general public. As one area mentioned in the manifesto was clima= te >> modeling, it is clear that enterprising non-scientists or muck-raking ty= pes >> can access these codes.**** >> >> **** >> >> In any well-commented code, there are bound to comments like "applying t= he >> Fandoozie trick" or other such innocucous statements. In addition, in a= ny >> code of over 1000 lines there are bound to be bugs. Can you imagine the >> public discourse when some rabel-rouser claims the software for climate >> modeling is flawed and he shows the offending code as "proof". Flaws an= d >> "tricks", common to all software, have the potential to be exploited for >> political gain under this manifesto.**** >> >> **** >> >> I'm not sure where the middle ground is when trying to make software ope= n, >> accessible, and maintaining peer review without the introduction of >> politics. I think this needs a lot more thought and consideration.**** >> >> Mark Zottola**** >> > > --0022158df36fc9b84c04af972bb9 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Excuse me? Is this the 10 minute argument or the full half hour?

On Tue, Oct 18, 2011 at 11:47 AM, Mark Zottola mzot= tola . gmail.com <owner-chemistry+/-ccl.net> wrote:
Jim,
=A0
The fact that an email mentioning a statistical "trick" for = analyzing the climate data caused a brouhaha was inane.=A0 As a scientist, = i have no problem saying a trick - beit computational or experimental - sol= ved a problem because no one in a scientific audience would interpret that = word to mean anything other than some slight cleverness to achieve a goal.= =A0 To the Luddites, a=A0trick is a lie and therefore the scientists are us= ing lies.=A0
=A0
It is not elitist in this atmosphere to be concerned about what peop= le who deliberately twist words will do with comments in the code.=A0 The f= act is that we live in an anti-scientific world where the severe exercise o= f reason (i.e. science) is displaced by gut feelings and other idiotic nons= equitirs by the obscuratum.=A0 As far as professionalism goes, as long as t= he code produces scientifically valid results, the content of comments shou= ld not be a concern to anyone.

On Tue, Oct 18, 2011 at 11:49 AM, Jim Kress ccl_= nospam*o*kressworks.com= <owner-chemistry-.-ccl.net> wrote:

Oh yeah.=A0 We can=92t let the great unwashed masses= view our code.=A0 They are so dumb.=A0 We might be embarrassed.=A0 /sarcas= m

=A0

That kind of elitist attitude is why many people hav= e lost faith in the Science that is being promulgated today.=A0 Elitism has= no place in Science.=A0 We are supposed to be professionals, not oracles.<= u>

=A0

If you are ashamed of the whimsy you place in the co= mments in the code, then don=92t put it there.=A0 Perhaps exposure to the p= ublic will lead to more professionalism in what we produce.

=A0

Jim Kress

= =A0

= =A0

From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com(a)ccl.net [mailto:owner-chemistry+ccl_nospam= =3D=3Dkressworks.com(a)ccl.net] On Behal= f Of Mark Zottola mzottola{=3D}gmail.com
Sent: Monday, October 17, 2011 9:09 PM
To: Kress, Jim
= Subject: CCL: Science code manifesto

<= /div>

=A0

For all our concerns about the impact of this manife= sto on science, I think most are missing what I believe to be an important = aspect.=A0 If a code is readily available for the scientific public, then i= t is readily available to the general public.=A0 As one area mentioned in t= he manifesto was climate modeling, it is clear that enterprising non-scient= ists or muck-raking types can access these codes.

=A0

In any well-commented code, there are bound to comme= nts like "applying the Fandoozie trick" or other such innocucous = statements.=A0 In addition, in any code of over 1000 lines there are bound = to be bugs.=A0 Can you imagine the public discourse when some rabel-rouser = claims the software for climate modeling is flawed and he shows the offendi= ng code as "proof".=A0 Flaws and "tricks", common to al= l software, have the potential to be exploited for political gain under thi= s manifesto.

=A0

I'm not sure where = the middle ground is when trying to make software open, accessible, and mai= ntaining peer review without the introduction of politics.=A0 I think this = needs a lot more thought and consideration.

Mark Zottola



--0022158df36fc9b84c04af972bb9-- From owner-chemistry@ccl.net Tue Oct 18 16:38:01 2011 From: "David A Mannock dmannock]^[ualberta.ca" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45685-111018144640-15615-RC7buUgoWb+fmXydE5uJ6A=server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=00248c0eee4e463ad704af9724ad Date: Tue, 18 Oct 2011 12:46:30 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock__ualberta.ca] --00248c0eee4e463ad704af9724ad Content-Type: text/plain; charset=ISO-8859-1 I am not going to disagree with Mark's comments as he makes some good points. However, as a Monty Python fan myself, I think the football game between the German and Greek philosophers in which no one actually kicks the ball, may be a more appropriate analogy. Dave http://www.youtube.com/watch?v=ur5fGSBsfq8 On Tue, Oct 18, 2011 at 6:51 AM, Mark Zottola mzottola ~ gmail.com < owner-chemistry-#-ccl.net> wrote: > "Although politics may be important in climate modeling, I thought that > this was the computer chemistry forum." > > Monte Python once did a skit that you never know when the Spanish > Inquisition will show up. I used weather modeling as an example, but the > bigger point is that who knows what ox is next to be gored. Computational > chemistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the > next battleground the luddites in the US would latch on to. Or > > There seems to be a yin and a yang to this idea. Full disclosure of > everything to anyone sounds good. But there are business concerns to be > addressed - can you imagine Gaussian putting their code in for full public > scrutiny? Government scientists using home grown codes face publication > issues due to overzealous Public Affairs Officers or their superiors > refusing to release codes in the vague name of national security. > Similarly, in closed systems like China who may refuse publication of their > internally developed codes, would we lose significant knowledge because we > refused to accept their papers due to this "manifesto"? Finally, the > specter of Mencken's booboise misusing that access to information. > > On the other hand, the QCPE was a great idea, but it seems to have died in > the academic rush to make money. Having codes readily available for > dissemination and use would be a positive for the community. > > Total non disclosure, copyrighting and hiding codes does seem to protect > the economic interests of those who have excelled in making money off their > codes. It sanctifies the current economic model used for making money in > computational chemistry. While there are benefits to this mixture of > economics and secrecy, the question is whether this is consistent with the > goals of science. > > The current two-tiered system in place - some software available for public > scrutiny, others protected as though it were the secret to the universe > probably does need some tweaking. But it is hard to see how a far-ranging > manifesto like this is going to solve much considering the utter disruption > its full implementation would cause. > > On Tue, Oct 18, 2011 at 1:42 AM, David A Mannock dmannock[a]ualberta.ca < > owner-chemistry###ccl.net> wrote: > >> Although politics may be important in climate modeling, I thought that >> this was the computer chemistry forum. OK, so some chemistry happens in the >> atmosphere, but accurate simulations of those conditions are also important. >> Whether a scientist or a member of the public finds an error in such code >> may not be important, although it does not help when people make mistakes. >> Science works iteratively, through criticism from all sides. Where I see a >> problem politically is where people (especially those in science) have >> models that they have spent years working on and whose funding is dependent >> on those models. Not disclosing experimental protocols/computer chemistry >> codes maintains secrecy and it becomes more difficult to break down a poor >> model. I have fought this in science for 30 years and it is hard work. We >> are all dependent on peoples honesty and integrity, and if this info is >> disclosed when the manuscript is submitted for publication, bad code or >> unclear justification of the code can be parsed by the reviewers and >> clarification requested. It does not help where there is a conflict of >> interest between the reviewer and the authors of the MS, but that is the >> Editors job. >> >> It is easy to make an argument for doing nothing, governments and >> universities across the world have raised this response to an art form. Is >> this something that we should accept and be happy about? >> >> >> On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=}gmail.com < >> owner-chemistry*ccl.net> wrote: >> >>> For all our concerns about the impact of this manifesto on science, I >>> think most are missing what I believe to be an important aspect. If a code >>> is readily available for the scientific public, then it is readily available >>> to the general public. As one area mentioned in the manifesto was climate >>> modeling, it is clear that enterprising non-scientists or muck-raking types >>> can access these codes. >>> >>> In any well-commented code, there are bound to comments like "applying >>> the Fandoozie trick" or other such innocucous statements. In addition, in >>> any code of over 1000 lines there are bound to be bugs. Can you imagine the >>> public discourse when some rabel-rouser claims the software for climate >>> modeling is flawed and he shows the offending code as "proof". Flaws and >>> "tricks", common to all software, have the potential to be exploited for >>> political gain under this manifesto. >>> >>> I'm not sure where the middle ground is when trying to make software >>> open, accessible, and maintaining peer review without the introduction of >>> politics. I think this needs a lot more thought and consideration. >>> >>> Mark Zottola >>> >> >> > --00248c0eee4e463ad704af9724ad Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am not going to disagree with Mark's comments as he makes some good p= oints. However, as a Monty Python fan myself, I think the football game bet= ween the German and Greek philosophers in which no one actually kicks the b= all, may be a more appropriate analogy. Dave

http://www.you= tube.com/watch?v=3Dur5fGSBsfq8

On Tue= , Oct 18, 2011 at 6:51 AM, Mark Zottola mzottola ~ gmail.com <owner-chemistry-#-ccl.net> wrote:
"Although politics may be importa= nt in climate modeling, I thought that this was the computer chemistry foru= m."
=A0
Monte Python once did a skit that you never know when th= e Spanish Inquisition will show up.=A0 I used weather modeling as an exampl= e, but the bigger point is that who knows what ox is next to be gored.=A0= =A0Computational chemistry studies (QM, MM/MD, QMD etc.) on methane clathra= tes could be the next battleground the=A0luddites in the US would latch on = to.=A0 Or =A0
=A0
There seems to be a yin and a yang to this idea.=A0 Full= disclosure of everything to anyone sounds good.=A0 But there are business = concerns to be addressed - can you imagine Gaussian putting their code in f= or full public scrutiny?=A0 Government scientists using home grown codes fa= ce publication issues due to overzealous Public Affairs Officers or their s= uperiors refusing to release codes in the vague name of national security.= =A0 Similarly, in closed systems like China who may refuse publication of t= heir internally developed codes, would we lose significant knowledge becaus= e we refused to accept their papers due to this "manifesto"?=A0 F= inally, the specter of Mencken's booboise misusing that access to infor= mation.
=A0
On the other hand, the QCPE was a great idea, but it see= ms to have died in the academic rush to make money.=A0 Having codes readily= available for dissemination and use would be a positive for the community.=
=A0
Total non disclosure, copyrighting and hiding codes does= seem to protect the economic interests of those who have excelled in makin= g money off their codes.=A0 It sanctifies the current economic model used f= or making money in computational chemistry.=A0 While there are benefits to = this mixture of economics and secrecy, the question is whether this is cons= istent with the goals of science.=A0
=A0
The current two-tiered system in place - some software a= vailable for public scrutiny, others protected as though it were the secret= to the universe probably does need some tweaking.=A0 But it is hard to see= how a far-ranging manifesto like this is going to solve much considering t= he utter disruption its full implementation would cause.

On Tue, Oct 18, 2011 at 1:42 AM, David= A Mannock dmannock[a]ualb= erta.ca <owner-chemistry###ccl.net> wrote:
Although politics may be important in climate modeling, = I thought that this was the computer chemistry forum. OK, so some chemistry= happens in the atmosphere, but accurate simulations of those conditions ar= e also important. Whether a scientist or a member of the public finds an er= ror in such code may not be important, although it does not help when peopl= e make mistakes. Science works iteratively, through criticism from all side= s. Where I see a problem politically is where people (especially those in s= cience) have models that they have spent years working on and whose funding= is dependent on those models. Not disclosing experimental protocols/comput= er chemistry codes maintains secrecy and it becomes more difficult to break= down a poor model. I have fought this in science for 30 years and it is ha= rd work. We are all dependent on peoples honesty and integrity, and if this= info is disclosed when the manuscript is submitted for publication, bad co= de or unclear justification of the code can be parsed by the reviewers and = clarification requested. It does not help where there is a conflict of inte= rest between the reviewer and the authors of the MS, but that is the Editor= s job.

It is easy to make an argument for doing nothing, governments and unive= rsities across the world have raised this response to an art form. Is this = something that we should accept and be happy about?


On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=3D}gmail.com <owner-chemistry*ccl.n= et> wrote:
For all our concerns about the impact of this manifesto on science, I = think most are missing what I believe to be an important aspect.=A0 If a co= de is readily available for the scientific public, then it is readily avail= able to the general public.=A0 As one area mentioned in the manifesto was c= limate modeling, it is clear that enterprising non-scientists or muck-rakin= g types can access these codes.
=A0
In any well-commented code, there are bound to comments = like "applying the Fandoozie trick" or other such innocucous stat= ements.=A0 In addition, in any code of over 1000 lines there are bound to b= e bugs.=A0 Can you imagine the public discourse when some rabel-rouser clai= ms the software for climate modeling is flawed and he shows the offending c= ode as "proof".=A0 Flaws and "tricks", common to all so= ftware, have the potential to be exploited for political gain under this ma= nifesto.
=A0
I'm not sure where the middle ground is when trying = to make software open, accessible, and maintaining peer review without the = introduction of politics.=A0 I think this needs a lot more thought and cons= ideration.

Mark Zottola



--00248c0eee4e463ad704af9724ad-- From owner-chemistry@ccl.net Tue Oct 18 17:13:01 2011 From: "=?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= adrian.cereto,+,gmail.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45686-111018101757-684-AvL1uvvrFpGm3f0cBUM5GQ]![server.ccl.net> X-Original-From: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= Content-Type: multipart/alternative; boundary=f46d04462e8a628a0e04af936328 Date: Tue, 18 Oct 2011 16:17:29 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= [adrian.cereto[A]gmail.com] --f46d04462e8a628a0e04af936328 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I don't think the manifesto is at odds with FSF. GPL'd software can be sold at any price, but its source code must be available for those who own the software at no further cost. And someone who has bought some GPL software i= s allowed to redistribute it for free, so researchers using it for a paper would be able to provide the software to reviewers and readers of the paper at no cost. El 17 d=E2=80=99octubre de 2011 18:42, Andrew Dalke dalke . dalkescientific= .com < owner-chemistry(!)ccl.net> ha escrit: > > Sent to CCL by: Andrew Dalke [dalke%dalkescientific.com] > On Oct 14, 2011, at 11:18 PM, Brian.James.Duke{:}gmail.com wrote: > > I just encountered the Science Code Manifesto, which essentially states > > that all computer code used for scientific analysis and modeling should > > be available for review. > > To be precise: > > All source code written specifically to process data > for a published paper must be available to the reviewers > and readers of the paper. > > I interpret that to mean that you don't need to ship source > code for the entire operating system, analysis tools, compiler, > and so on. For that matter, you can publish your Gaussian > script, and not need to include the source for Gaussian itself. > > It does seems like it leaves a hole for people who write > a general purpose program for one project, then use it > (unchanged) for something which is published. Of course, the > editors may object to that practice. > > > There's also a problem with: > > Researchers who use or adapt science source code in > their research must credit the code=E2=80=99s creators in > resulting publications > > Consider the 70 authors and 15 libraries which make up > the CDK chemistry toolkit. There might be 100+ creators. > It's beyond reason to include everyone in the publications, > and the general expectation is to reference the project, > not all of the code's creators. > > Finally, if you are a follower of the Free Software Foundation's > ideas on software freedom, then you agree that there's a freedom > to sell software (http://www.gnu.org/philosophy/selling.html ) > for as much money as you want. This manifesto is almost at odds > with the FSF viewpoint; I see it omits any discussion of how > much it should cost to access the curated software. > > These aren't big problems, but they do point out that this > is a complex issue. > > Andrew Dalke > dalke(~)dalkescientific.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --f46d04462e8a628a0e04af936328 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I don't think the manifesto is at odds with FSF. GPL'd software can= be sold at any price, but its source code must be available for those who = own the software at no further cost. And someone who has bought some GPL so= ftware is allowed to redistribute it for free, so researchers using it for = a paper would be able to provide the software to reviewers and readers of t= he paper at no cost.

El 17 d=E2=80=99octubre de 2011 18:42, Andre= w Dalke dalke . dalkescientific.com<= /a> <owner-= chemistry(!)ccl.net> ha escrit:

Sent to CCL by: Andrew Dalke [dalke%dalkescientific.com]
On Oct 14, 2011, at 11:18 PM, Brian.James.Duke{:}gmail.com wrote:
> I just encountered the Science Code Manifesto, which essentially state= s
> that all computer code used for scientific analysis and modeling shoul= d
> be available for review.

To be precise:

=C2=A0All source code written specifically to process data
=C2=A0for a published paper must be available to the reviewers
=C2=A0and readers of the paper.

I interpret that to mean that you don't need to ship source
code for the entire operating system, analysis tools, compiler,
and so on. For that matter, you can publish your Gaussian
script, and not need to include the source for Gaussian itself.

It does seems like it leaves a hole for people who write
a general purpose program for one project, then use it
(unchanged) for something which is published. Of course, the
editors may object to that practice.


There's also a problem with:

=C2=A0 =C2=A0Researchers who use or adapt science source code in
=C2=A0 =C2=A0their research must credit the code=E2=80=99s creators in
=C2=A0 =C2=A0resulting publications

Consider the 70 authors and 15 libraries which make up
the CDK chemistry toolkit. There might be 100+ creators.
It's beyond reason to include everyone in the publications,
and the general expectation is to reference the project,
not all of the code's creators.

Finally, if you are a follower of the Free Software Foundation's
ideas on software freedom, then you agree that there's a freedom
to sell software (http://www.gnu.org/philosophy/selling.html )
for as much money as you want. This manifesto is almost at odds
with the FSF viewpoint; I see it omits any discussion of how
much it should cost to access the curated software.

These aren't big problems, but they do point out that this
is a complex issue.

=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=A0Andrew Dalke
=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=A0dalke(~)dalkescientific.com



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(!)ccl.n= et or use:
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--f46d04462e8a628a0e04af936328-- From owner-chemistry@ccl.net Tue Oct 18 17:49:01 2011 From: "Jiabo Li jiaboli,,yahoo.com" To: CCL Subject: CCL: MO overlap CASSCF Message-Id: <-45687-111018152053-24917-2oP+AU+/QiXKvQgxckNMYA=server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="-2114655128-1742780897-1318965586=:13153" Date: Tue, 18 Oct 2011 12:19:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli(_)yahoo.com] ---2114655128-1742780897-1318965586=:13153 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable The orbitals in any MO-based calculations are orthogonal. Therefore, any tw= o different orbitals in CASSCF space are orthogonal, i.e. the overlay inter= gral is zero. If you are interested in non-orthogonal CAS calculation, whic= h allows you to have maximal localized orbitals, you can try CASVB method i= n VB2000 program, which can be found at http://www.vb2000.net=0A=A0=0AJiabo= Li=0A=0A=0A________________________________=0AFrom: Robert Perkins cclnano= lab(!)gmail.com =0ATo: "Li, Jiabo " =0ASent: Tuesday, October 18, 2011 10:39 AM=0ASubject: CCL: MO= overlap CASSCF=0A=0A=0ADear All,=0AI would like to calculate overlap integ= ral of two orbitals in CAS calculations. Do you know how to do that in G09?= =0ABest regards=0AR.P. ---2114655128-1742780897-1318965586=:13153 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
The orbitals in any MO-based calculations= are orthogonal. Therefore, any two different orbitals in CASSCF space are = orthogonal, i.e. the overlay intergral is zero. If you are interested in no= n-orthogonal CAS calculation, which allows yo= u to have maximal localized orbitals, you can try CASVB method in VB2000 pr= ogram, which can be found at http://www.v= b2000.net
 
Jiabo Li

From:= Robert Perkins cclnanolab(!)gmail.com <owner-chemistry(0)ccl.n= et>
To: "Li, Jiabo -i= d#3p9-" <jiaboli(0)yahoo.com>
S= ent: Tuesday, October 18, 2011 10:39 AM
Subject: CCL: MO overlap CASSCF

Dear All,
I would like to calculate overlap integ= ral of two orbitals in CAS calculations. Do you know how to do that in G09?=
Best regards
R.P.


---2114655128-1742780897-1318965586=:13153-- From owner-chemistry@ccl.net Tue Oct 18 18:24:00 2011 From: "Nuno A. G. Bandeira nuno.bandeira+/-ist.utl.pt" To: CCL Subject: CCL:G: MO overlap CASSCF Message-Id: <-45688-111018154359-29204-3NFRUlseiyP5otACz449wQ^-^server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Tue, 18 Oct 2011 20:43:36 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira,ist.utl.pt] On 18-10-2011 18:39, Robert Perkins cclnanolab(!)gmail.com wrote: > Dear All, > I would like to calculate overlap integral of two orbitals in CAS > calculations. Do you know how to do that in G09? > Best regards > R.P. I think you need to use iop(3/36=20) for more see here: http://www.gaussian.com/g_tech/g_iops/ov3.htm -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- From owner-chemistry@ccl.net Tue Oct 18 18:58:00 2011 From: "Mark Zottola mzottola_-_gmail.com" To: CCL Subject: CCL:G: Science code manifesto Message-Id: <-45689-111018150259-4168-nANl1vHuUK5L3Wevg0uu4Q||server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=bcaec520f08583375604af975e71 Date: Tue, 18 Oct 2011 15:02:47 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola|gmail.com] --bcaec520f08583375604af975e71 Content-Type: text/plain; charset=ISO-8859-1 In the military it happens all the time. My question is, if the DOD decides a code cannot be released, and this mnifesto is in effect, then what happens to that DOD paper? What happens to be that science? As far as your estimation of "classified science", you are naive. The DOD can and often does assume everything is secret unless otherwise decreed. NON-classified, publicly funded research inside the DOD cannot be divulged without PAO approval. Again, your assumption about classification is far from reality. It is not much of an assumption that scientists are principled when it comes to reporting science. Why should we lose their contributions due to a manifesto. And indeed, you failed to address the other point I made - if Chinese reserchers cannot publish their code, do we ignore their contribution because of this manifesto? I do not believe it is unreasonable to ask about the overall effects of a de facto policy about full public disclosure. And indeed you do gloss over the problems of proprietary code and the conflict between profit and principle. For now, open source is the best we can hope for, but I am indeed open to other mechanisms. But a straight jacket in terms of a manifesto seems to be antithetical to science and poorly thought out. On Tue, Oct 18, 2011 at 11:57 AM, N. Sukumar nagams(!)rpi.edu < owner-chemistry_._ccl.net> wrote: > > Sent to CCL by: "N. Sukumar" [nagams**rpi.edu] > Economic and national security concerns could be legitimate issues, but > hiding science from the public (who pays for it) in order to protect it > > from luddites or from political attacks is the most ridiculous thing I've > heard yet. They used to do something like that in the Dark Ages, hiding > whatever science there was behind magic spells, rites of initiation and > oaths of secrecy - and we know how well science flourished during those > times. They were called the Dark Ages for a reason! At best such tactics > will be counter-productive and discredit such secret scientific results. > It would then truly be a case of My (Holy) Book versus Your Book! > > As I read it, the manifesto only applies to results meant for > publication. Since classified defense research does not generally make it > into publication, the issue would therefore be moot with regard to > genuine national security concerns. And yes, I can imagine Gaussian > making their code available for public scrutiny. In fact, they do so now; > many scientists around the world have access to and are able to > scrutinize the source code, or even modify it for their private use. > Their restrictions concern reproduction (copyright), redistribution, > re-engineering and publication of benchmarks related to performance, not > whether there are bugs in the algorithm or not. > > It was also mentioned in this discussion that journal editors/reviewers > do not have the time or resources to verify source code or reproduce > results and that you cannot expect a research group to shut down their > lab while you try to reproduce their results on their systems. By and > large this is generally true, but in cases of exceptional > interest/importance (e.g. the case of homeopathy), Nature for instance > has been known to send out a team of editors/reviewers to do just that. > However, it is unrealistic to expect unpaid reviewers to bear the full > responsibility for fact-checking all the intricate details of the code > used to generate scientific results. On the whole, this works best by the > self-correcting, re-engineering, crowd-sourcing nature of the scientific > enterprise, but having the raw data and source code available for > inspection in those exceptional circumstances (as in the example above or > as in the case of anthropocentric global warming) is important for > ensuring transparency and confidence in the scientific results. > > Dr. N. Sukumar > Rensselaer Exploratory Center for Cheminformatics Research > http://reccr.chem.rpi.edu/ -------------------------- > "A Drug is any substance which, when injected into a rat, produces a > publishable, scientific paper." > > > ==============Original message text=============== > On Tue, 18 Oct 2011 8:51:41 EDT "Mark Zottola mzottola ~ gmail.com" > wrote: > > "Although politics may be important in climate modeling, I thought that > this > was the computer chemistry forum." > > Monte Python once did a skit that you never know when the Spanish > Inquisition will show up. I used weather modeling as an example, but the > bigger point is that who knows what ox is next to be gored. Computational > chemistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the > next battleground the luddites in the US would latch on to. Or > > There seems to be a yin and a yang to this idea. Full disclosure of > everything to anyone sounds good. But there are business concerns to be > addressed - can you imagine Gaussian putting their code in for full public > scrutiny? Government scientists using home grown codes face publication > issues due to overzealous Public Affairs Officers or their superiors > refusing to release codes in the vague name of national security. > Similarly, in closed systems like China who may refuse publication of their > internally developed codes, would we lose significant knowledge because we > refused to accept their papers due to this "manifesto"? Finally, the > specter of Mencken's booboise misusing that access to information. > > On the other hand, the QCPE was a great idea, but it seems to have died in > the academic rush to make money. Having codes readily available for > dissemination and use would be a positive for the community. > > Total non disclosure, copyrighting and hiding codes does seem to protect > the > economic interests of those who have excelled in making money off their > codes. It sanctifies the current economic model used for making money in > computational chemistry. While there are benefits to this mixture of > economics and secrecy, the question is whether this is consistent with the > goals of science. > > The current two-tiered system in place - some software available for public > scrutiny, others protected as though it were the secret to the universe > probably does need some tweaking. But it is hard to see how a far-ranging > manifesto like this is going to solve much considering the utter disruption > its full implementation would cause. > > On Tue, Oct 18, 2011 at 1:42 AM, David A Mannock dmannock[a]ualberta.ca < > owner-chemistry###ccl.net> wrote: > > > Although politics may be important in climate modeling, I thought that > this > > was the computer chemistry forum. OK, so some chemistry happens in the > > atmosphere, but accurate simulations of those conditions are also > important. > > Whether a scientist or a member of the public finds an error in such code > > may not be important, although it does not help when people make > mistakes. > > Science works iteratively, through criticism from all sides. Where I see > a > > problem politically is where people (especially those in science) have > > models that they have spent years working on and whose funding is > dependent > > on those models. Not disclosing experimental protocols/computer chemistry > > codes maintains secrecy and it becomes more difficult to break down a > poor > > model. I have fought this in science for 30 years and it is hard work. We > > are all dependent on peoples honesty and integrity, and if this info is > > disclosed when the manuscript is submitted for publication, bad code or > > unclear justification of the code can be parsed by the reviewers and > > clarification requested. It does not help where there is a conflict of > > interest between the reviewer and the authors of the MS, but that is the > > Editors job. > > > > It is easy to make an argument for doing nothing, governments and > > universities across the world have raised this response to an art form. > Is > > this something that we should accept and be happy about? > > > > > > On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{=}gmail.com < > > owner-chemistry*ccl.net> wrote: > > > >> For all our concerns about the impact of this manifesto on science, I > >> think most are missing what I believe to be an important aspect. If a > code > >> is readily available for the scientific public, then it is readily > available > >> to the general public. As one area mentioned in the manifesto was > climate > >> modeling, it is clear that enterprising non-scientists or muck-raking > types > >> can access these codes. > >> > >> In any well-commented code, there are bound to comments like "applying > the > >> Fandoozie trick" or other such innocucous statements. In addition, in > any > >> code of over 1000 lines there are bound to be bugs. Can you imagine the > >> public discourse when some rabel-rouser claims the software for climate > >> modeling is flawed and he shows the offending code as "proof". Flaws > and > >> "tricks", common to all software, have the potential to be exploited for > >> political gain under this manifesto. > >> > >> I'm not sure where the middle ground is when trying to make software > open, > >> accessible, and maintaining peer review without the introduction of > >> politics. I think this needs a lot more thought and consideration. > >> > >> Mark Zottola > >> > > > > > ===========End of original message text===========> > > --bcaec520f08583375604af975e71 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
In the military it happens all the time.=A0 My question is, if the DOD= decides a code cannot be released, and this mnifesto is in effect, then wh= at happens to that DOD paper?=A0 What happens to be that science?=A0 As far= as your estimation of "classified science", you are naive.=A0 Th= e DOD can and often does assume everything is secret unless otherwise decre= ed.=A0 NON-classified, publicly funded research inside the DOD cannot be di= vulged without PAO approval.=A0 Again, your assumption about classification= is far from reality.
=A0
It is not much of an assumption that scientists are principled when it= comes to reporting science.=A0 Why should we lose their contributions due = to a manifesto.=A0 And indeed, you failed to address the other point I made= - if Chinese reserchers cannot publish their code, do we ignore their cont= ribution because of this manifesto?
=A0
I do not believe it is unreasonable to ask about the overall effects o= f a de facto policy about full public disclosure.=A0 And indeed you do glos= s over the problems of proprietary code and the conflict between profit and= principle.
=A0
For now, open source is the best we can hope for, but I am indeed open= to other mechanisms.=A0 But a straight jacket in terms of a manifesto seem= s to be antithetical to science and poorly thought out.=A0
On Tue, Oct 18, 2011 at 11:57 AM, N. Sukumar nag= ams(!)rpi.edu <owner-chemistry_._ccl.net> = wrote:

Sent to CCL by: "N. Suk= umar" [nagams**rpi.edu]
Economic and national security concerns could be legitimate issues, but
= hiding science from the public (who pays for it) in order to protect it
= > from luddites or from political attacks is the most ridiculous thing I= 've
heard yet. They used to do something like that in the Dark Ages, hiding
= whatever science there was behind magic spells, rites of initiation and
= oaths of secrecy - and we know how well science flourished during those
times. They were called the Dark Ages for a reason! At best such tacticswill be counter-productive and discredit such secret scientific results.It would then truly be a case of My (Holy) Book versus Your Book!

As I read it, the manifesto only applies to results meant for
public= ation. Since classified defense research does not generally make it
into= publication, the issue would therefore be moot with regard to
genuine n= ational security concerns. And yes, I can imagine Gaussian
making their code available for public scrutiny. In fact, they do so now;many scientists around the world have access to and are able to
scruti= nize the source code, or even modify it for their private use.
Their res= trictions concern reproduction (copyright), redistribution,
re-engineering and publication of benchmarks related to performance, notwhether there are bugs in the algorithm or not.

It was also mention= ed in this discussion that journal editors/reviewers
do not have the tim= e or resources to verify source code or reproduce
results and that you cannot expect a research group to shut down their
l= ab while you try to reproduce their results on their systems. By and
lar= ge this is generally true, but in cases of exceptional
interest/importan= ce (e.g. the case of homeopathy), Nature for instance
has been known to send out a team of editors/reviewers to do just that.
= However, it is unrealistic to expect unpaid reviewers to bear the full
r= esponsibility for fact-checking all the intricate details of the code
used to generate scientific results. On the whole, this works best by theself-correcting, re-engineering, crowd-sourcing nature of the scientific<= br>enterprise, but having the raw data and source code available for
inspection in those exceptional circumstances (as in the example above oras in the case of anthropocentric global warming) is important for
ens= uring transparency and confidence in the scientific results.

Dr. N. = Sukumar
Rensselaer Exploratory Center for Cheminformatics Research
http://reccr.chem.rpi.edu/ = --------------------------
"A Drug is any substance which, when inj= ected into a rat, produces a
publishable, scientific paper."


=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3DOriginal message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D
On Tue, 18 Oct 2011 8:51:41 EDT "Mark Zottola mzotto= la ~ gmail.com" wr= ote:

"Although politics may be important in climate modeling, I= thought that this
was the computer chemistry forum."

Monte Python once did a skit= that you never know when the Spanish
Inquisition will show up. =A0I use= d weather modeling as an example, but the
bigger point is that who knows= what ox is next to be gored. =A0Computational
chemistry studies (QM, MM/MD, QMD etc.) on methane clathrates could be the<= br>next battleground the luddites in the US would latch on to. =A0Or
There seems to be a yin and a yang to this idea. =A0Full disclosure of
everything to anyone sounds good. =A0But there are business concerns to be<= br>addressed - can you imagine Gaussian putting their code in for full publ= ic
scrutiny? =A0Government scientists using home grown codes face public= ation
issues due to overzealous Public Affairs Officers or their superiors
ref= using to release codes in the vague name of national security.
Similarly= , in closed systems like China who may refuse publication of their
inter= nally developed codes, would we lose significant knowledge because we
refused to accept their papers due to this "manifesto"? =A0Finall= y, the
specter of Mencken's booboise misusing that access to informa= tion.

On the other hand, the QCPE was a great idea, but it seems to = have died in
the academic rush to make money. =A0Having codes readily available for
d= issemination and use would be a positive for the community.

Total no= n disclosure, copyrighting and hiding codes does seem to protect the
eco= nomic interests of those who have excelled in making money off their
codes. =A0It sanctifies the current economic model used for making money in=
computational chemistry. =A0While there are benefits to this mixture of=
economics and secrecy, the question is whether this is consistent with = the
goals of science.

The current two-tiered system in place - some soft= ware available for public
scrutiny, others protected as though it were t= he secret to the universe
probably does need some tweaking. =A0But it is= hard to see how a far-ranging
manifesto like this is going to solve much considering the utter disruption=
its full implementation would cause.

On Tue, Oct 18, 2011 at 1:4= 2 AM, David A Mannock dmannock[a]ualberta.ca <
owner-chemistry###ccl.net= > wrote:

> Although politics may be important in climate model= ing, I thought that this
> was the computer chemistry forum. OK, so s= ome chemistry happens in the
> atmosphere, but accurate simulations of those conditions are also impo= rtant.
> Whether a scientist or a member of the public finds an error= in such code
> may not be important, although it does not help when = people make mistakes.
> Science works iteratively, through criticism from all sides. Where I s= ee a
> problem politically is where people (especially those in scien= ce) have
> models that they have spent years working on and whose fun= ding is dependent
> on those models. Not disclosing experimental protocols/computer chemis= try
> codes maintains secrecy and it becomes more difficult to break = down a poor
> model. I have fought this in science for 30 years and i= t is hard work. We
> are all dependent on peoples honesty and integrity, and if this info i= s
> disclosed when the manuscript is submitted for publication, bad c= ode or
> unclear justification of the code can be parsed by the revie= wers and
> clarification requested. It does not help where there is a conflict of=
> interest between the reviewer and the authors of the MS, but that = is the
> Editors job.
>
> It is easy to make an argument = for doing nothing, governments and
> universities across the world have raised this response to an art form= . Is
> this something that we should accept and be happy about?
&g= t;
>
> On Mon, Oct 17, 2011 at 7:09 PM, Mark Zottola mzottola{= =3D}gmail.com <
> owner-chemistry*ccl.net<= /a>> wrote:
>
>> For all our concerns about the impact of= this manifesto on science, I
>> think most are missing what I bel= ieve to be an important aspect. =A0If a code
>> is readily available for the scientific public, then it is readily= available
>> to the general public. =A0As one area mentioned in t= he manifesto was climate
>> modeling, it is clear that enterprisin= g non-scientists or muck-raking types
>> can access these codes.
>>
>> In any well-commen= ted code, there are bound to comments like "applying the
>> F= andoozie trick" or other such innocucous statements. =A0In addition, i= n any
>> code of over 1000 lines there are bound to be bugs. =A0Can you ima= gine the
>> public discourse when some rabel-rouser claims the sof= tware for climate
>> modeling is flawed and he shows the offending= code as "proof". =A0Flaws and
>> "tricks", common to all software, have the potential to = be exploited for
>> political gain under this manifesto.
>&g= t;
>> I'm not sure where the middle ground is when trying to m= ake software open,
>> accessible, and maintaining peer review without the introduction o= f
>> politics. =A0I think this needs a lot more thought and consid= eration.
>>
>> Mark Zottola
>>
>
>
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