From owner-chemistry@ccl.net Wed Mar 2 00:08:01 2022 From: "Sachin Ramesh sachinadityaramesh#,#gmail.com" To: CCL Subject: CCL: Best way to visualize charge densities Message-Id: <-54617-220301223727-11204-43h8eXmuNQNdqi/yCtRj2g__server.ccl.net> X-Original-From: Sachin Ramesh Content-Type: multipart/alternative; boundary="000000000000c266e805d933ff7a" Date: Wed, 2 Mar 2022 09:07:40 +0530 MIME-Version: 1.0 Sent to CCL by: Sachin Ramesh [sachinadityaramesh!=!gmail.com] --000000000000c266e805d933ff7a Content-Type: text/plain; charset="UTF-8" Anson, You could also look at UCSF Chimera. Available here, https://www.cgl.ucsf.edu/chimera/ It works for cube files. Hope this helps -Sachin On Wed, Mar 2, 2022 at 1:14 AM Anson Thomas thomasanson53##gmail.com < owner-chemistry-$-ccl.net> wrote: > Dear CCL members, > > I have obtained cube files of charge density difference using Quantum > Espresso. I am trying to plot these as a contour plot in an aesthetically > pleasing manner with good quality. I'm aware that XCrsyDen could do this, > but the resolution of the exported file isn't good. Also tried Vesta, but > was not satisfied with the results. > I desire to plot something like figure 5 in this paper ( > https://doi.org/10.1186/s11671-018-2605-3). Is there some other > software/piece of code that can help accomplish similar results? > > Any help would be appreciated. > > Sincerely, > Anson > > > > -- > *Anson Thomas* > M.Sc. Chemistry, IIT Roorkee > https://www.linkedin.com/in/ansonthms/ > --000000000000c266e805d933ff7a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Anson,
=C2=A0=C2=A0
=C2=A0 =C2=A0 You could = also look at UCSF Chimera.=C2=A0
Available=C2=A0here,=C2=A0https://www.cgl.ucsf.edu/chimera/=C2= =A0
It works for cube files.=C2=A0
Hope this helps

-Sachin=C2=A0

On Wed, Mar 2, 2022 at 1:14 AM Anso= n Thomas thomasanson53##gmail.com <owner-chemistry-$-ccl.net> wrot= e:
Dear CCL members,

= I have obtained cube files of charge density difference using Quantum Espre= sso. I am trying to plot these as a contour plot in an aesthetically pleasi= ng=C2=A0manner with=C2=A0good quality. I'm aware that XCrsyDen could do= this, but the=C2=A0resolution of the exported file isn't good. Also tr= ied Vesta,=C2=A0but was not satisfied with the results.
I desire = to plot something like figure 5 in this paper (https://doi.org/10.1186/s11671-= 018-2605-3). Is there some other software/piece of code that can help a= ccomplish similar results?

Any help would be appre= ciated.=C2=A0

Sincerely,
Anson



--
Anson Thomas
M.Sc. Chemistry, IIT Roorkee
htt= ps://www.linkedin.com/in/ansonthms/
--000000000000c266e805d933ff7a-- From owner-chemistry@ccl.net Wed Mar 2 09:19:00 2022 From: "=?iso-8859-2?Q?Mariusz_Rado=F1?= mariusz.radon=uj.edu.pl" To: CCL Subject: CCL: Cloud backup in computational chemistry Message-Id: <-54618-220302060757-29189-ZJlsyfeNbMsydqnUonUZig#server.ccl.net> X-Original-From: =?iso-8859-2?Q?Mariusz_Rado=F1?= Content-ID: <33C2DAADB77F8E469C1F5FD5D1FC3065#eurprd04.prod.outlook.com> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 2 Mar 2022 11:07:45 +0000 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-2?Q?Mariusz_Rado=F1?= [mariusz.radon##uj.edu.pl] > On 1 Mar 2022, at 21:35, Detlev Conrad Mielczarek detlevcm#,#googlemail.com wrote: > > > Sent to CCL by: Detlev Conrad Mielczarek [detlevcm]![googlemail.com] > Please note, RAID is NOT a backup. > > The topic is fairly complex if done rigorously. Look up "bit rot" - data life is finite too. > Look up the risk of data corruption on a RAID system - or loss with say malware or error. > > The topic is not simple - unfortunately. > And then there is data lifetime on disks which is not necessarily a resolved question. > Tape is considered the best for long term storage at current - maybe archive quality DVDs. > > Detlev > > > > Sent from my BlackBerry > Dear All: Indeed, the topic is not simple. But considering the reliability of RAID, the crucial parameter is URE (unrecoverable read error rate) of the hard drives. This is especially important for big drives, like 6TB or larger. You can read more about URE and RAID on the net, for instance here: https://www.raid-failure.com/ Best wishes, Mariusz > > > Original Message > > >> From: owner-chemistry[*]ccl.net > Sent: 1 March 2022 21:19 > To: detlevcm[*]googlemail.com > Reply to: chemistry[*]ccl.net > Subject: CCL: Cloud backup in computational chemistry > > > Rather than cloud, may I suggest a 2 TB Raid system? They can be had for less than $200, and RAID 1 would provide adequate long-term stability. > > > Dan Strahs > > > > >> From: owner-chemistry+dstrahs==pace.edu##ccl.net on behalf of Rassolov, Vitaly RASSOLOV~!~mailbox.sc.edu > Sent: Tuesday, March 1, 2022 9:35 AM > To: Strahs, Dr. Daniel Bernard > Subject: CCL: Cloud backup in computational chemistry > > Open Science Framework https://www.cos.io stores data at $4000/TB, guaranteed for 50 years. I don't have any personal experience with it, and it seems pricey for an individual. If your institution is affiliated with the OSF, perhaps the price is different. > > Center for Open Science > At the Center for Open Science, our mission is to increase openness, integrity, and reproducibility of scholarly research. Promoting these practices within the research funding and publishing communities accelerates scientific progress > www.cos.io > > > > > Vitaly Rassolov > Department of Chemistry and Biochemistry > University of South Carolina > 631 Sumter St, Columbia SC 29208 > https://sc.edu/study/colleges_schools/chemistry_and_biochemistry/our_people/directory/rassolov_vitaly.php > >> From: owner-chemistry+rassolov==mail.chem.sc.edu=ccl.net on behalf of Andrew DeYoung andrewdaviddeyoung#%#gmail.com > Sent: Monday, February 28, 2022 4:48 PM > To: Rassolov, Vitaly > Subject: CCL: Cloud backup in computational chemistry > > Hi, > > > I have ~1.5 TB of analysis data on my home computer related to my PhD work, which I completed last year. I would like to put this data in long-term storage in the cloud. I will retain a backup on an external hard drive, which I will keep at home. But I'm looking for an additional backup in another location (the other location being, ideally, the cloud). These files are not themselves MD trajectories from my PhD, but rather are output and analyses related to the trajectories. (The trajectories themselves are tens of TB and are being retained, for now, by my university.) > > > Does anyone have experience with archiving scientific data on cloud storage services such as AWS S3, AWS S3 Glacier, Microsoft Azure, or iDrive? > > > I realize this is the Computational Chemistry List, not the Information Technology List, but I'd be grateful for any insight you may have from the perspective of a computational chemist. > > > I will be paying for this myself, so the service needs to be reasonably priced for a single user for ~5-10 TB or less. It's not immediately clear to me whether all of these services are really available to individuals. > > > I don't need fancy features like automatic backup, delta copying, and so forth; I just need a place to safely store some files. I use Linux for running computation, but I'm not an IT expert by any means; I am willing to learn, though, especially when good documentation is available! And, clearly, transferring ~1.5 TB to the cloud is itself a nontrivial task, but I'm willing to see what the options are. > > > Here are some links to some seemingly popular services in my country (US), but perhaps there are others more particularly suited for scientific data: > > > AWS Amazon S3: https://aws.amazon.com/s3/ > AWS Amazon S3 Glacier: https://aws.amazon.com/s3/storage-classes/glacier/ > Microsoft Azure: https://azure.microsoft.com/en-us/services/#storage > > iDrive: https://www.idrive.com/ > > > Thank you for your time! > > > Best, > Andrew > > Andrew DeYoung, PhD > Department of Chemistry > Carnegie Mellon University> > From owner-chemistry@ccl.net Wed Mar 2 12:26:01 2022 From: "Susi Lehtola susi.lehtola-$-alumni.helsinki.fi" To: CCL Subject: CCL: Cloud backup in computational chemistry Message-Id: <-54619-220302002227-16618-fP2ARbDalyuVwuscDc1M5Q]![server.ccl.net> X-Original-From: Susi Lehtola Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 2 Mar 2022 00:22:12 -0500 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola..alumni.helsinki.fi] On 3/1/22 15:35, Detlev Conrad Mielczarek detlevcm#,#googlemail.com wrote: > > Sent to CCL by: Detlev Conrad Mielczarek [detlevcm]![googlemail.com] > Please note, RAID is NOT a backup. > > The topic is fairly complex if done rigorously. Look up "bit rot" - data life is finite too. > Look up the risk of data corruption on a RAID system - or loss with say malware or error. > > The topic is not simple - unfortunately. > And then there is data lifetime on disks which is not necessarily a resolved question. > Tape is considered the best for long term storage at current - maybe archive quality DVDs. Yes, at the bare minimum you would want 2 NAS systems each running RAID 1, preferably with disk drives from different manufacturers. That way if there's a manufacturing error in a hard drive, it won't affect the whole array at once. But, an electrical failure or a fire would still wipe out the whole system. That's why you want backups in another physical location. I heard from an old Linux developer colleague that he had bunched up with a friend and set up a pair of home servers with 4 hard drives on RAID 5 each. They had encrypted partitions on each others' servers, which would be automatically be kept in sync: your home directory would also be encrypted onto your friend's server. You can't access their data, and they can't access your data, but you both enjoy the significant benefit of having your data automatically backed up elsewhere, and only have to put up the cost of setting up the servers if you can host a server in your home. -- ------------------------------------------------------------------ Mr. Susi Lehtola, PhD Adjunct Professor susi.lehtola|*|alumni.helsinki.fi University of Helsinki http://susilehtola.github.io/ Finland ------------------------------------------------------------------ Susi Lehtola, FT dosentti susi.lehtola|*|alumni.helsinki.fi Helsingin yliopisto http://susilehtola.github.io/ ------------------------------------------------------------------