Re: [Wien] A basic question regarding atomic coordinates optimization
Dear Prof. Marks & Prof. Gavin, Thank you for your responses. I will go through the study materials. with kind regards, On Mon, 4 Jul 2022 at 03:01, Laurence Marks wrote: > I need to rewrite the README. Having just looked at it fresh, it has > pieces from multiple releases hashed together in a way that few (perhaps > none) can understand. > > The PowerPoint at > http://www.numis.northwestern.edu/Presentations/MSR1a.pptx > Is better, but it has no words! > > Best at the moment is to read the most recent paper on the Predictive > mixing. > https://doi.org/10.1021/acs.jctc.1c00630 > > Maybe next week... > > -- > Professor Laurence Marks > Department of Materials Science and Engineering, Northwestern University > www.numis.northwestern.edu > "Research is to see what everybody else has seen, and to think what nobody > else has thought" Albert Szent-Györgyi > > On Sun, Jul 3, 2022, 3:09 PM Laurence Marks > wrote: > >> You should look at README_10.8, also at >> http://www.wien2k.at/reg_user/textbooks/README_10.8.pdf >> >> Unfortunately the one that Gavin cited is for constrained optimization, >> which is useful for finding barriers although still a little experimental. >> It does not give information on the structure optimization using MSR1a. >> (PORT is different; for that look up "quasi-Newton optimization".) >> >> For reference, in some respects MSR1, MSR1a and PORT are AI. They are not >> simple. >> >> -- >> Professor Laurence Marks >> Department of Materials Science and Engineering, Northwestern University >> www.numis.northwestern.edu >> "Research is to see what everybody else has seen, and to think what >> nobody else has thought" Albert Szent-Györgyi >> >> On Sun, Jul 3, 2022, 2:59 PM Gavin Abo wrote: >> >>> Not sure if it helpful or not, but should it be, there was a thread of >>> posts related to force minimization back in March of 2021, in it you can >>> see it references a "README_Constraints.pdf": >>> >>> >>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20952.html >>> >>> The README_Constraints.pdf appears to be identical to the "Constraint >>> structure optimization (pdf)" link which is on the WIEN2k webpage among >>> other structure optimization documentation (Structure optimization-notes, >>> Notes on the mixer, ...): >>> >>> http://www.wien2k.at/reg_user/textbooks/ >>> >>> Kind Regards, >>> Gavin >>> WIEN2k user >>> >>> On 7/3/2022 1:26 PM, shamik chakrabarti wrote: >>> >>> Dear Wien2k users, >>> I have a basic question. When the force at >>> each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) >>> & if the force at each atom is found to be larger than the cut-off values, >>> the shifting of atomic coordinates occurs for searching equilibrium. Now, >>> here the question arises: >>> >>> *How did the algorithm know which way to proceed? * >>> >>> For volume optimization, we fed the data of the lattice parameters & the >>> code performs the calculation on the same. But during force minimization, >>> we did not feed the values of atomic coordinates apart from the initial >>> values, still the code search for new atomic coordinates spontaneously? Is >>> it AI? >>> >>> Looking forward to your reply >>> >>> with regards, >>> >>> -- >>> Dr. Shamik Chakrabarti >>> Research Fellow >>> Department of Physics >>> Indian Institute of Technology Patna >>> Bihta-801103 >>> Patna >>> Bihar, India >>> >>> ___ >>> Wien mailing list >>> Wien@zeus.theochem.tuwien.ac.at >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>> SEARCH the MAILING-LIST at: >>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>> >> ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] A basic question regarding atomic coordinates optimization
I need to rewrite the README. Having just looked at it fresh, it has pieces from multiple releases hashed together in a way that few (perhaps none) can understand. The PowerPoint at http://www.numis.northwestern.edu/Presentations/MSR1a.pptx Is better, but it has no words! Best at the moment is to read the most recent paper on the Predictive mixing. https://doi.org/10.1021/acs.jctc.1c00630 Maybe next week... -- Professor Laurence Marks Department of Materials Science and Engineering, Northwestern University www.numis.northwestern.edu "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Györgyi On Sun, Jul 3, 2022, 3:09 PM Laurence Marks wrote: > You should look at README_10.8, also at > http://www.wien2k.at/reg_user/textbooks/README_10.8.pdf > > Unfortunately the one that Gavin cited is for constrained optimization, > which is useful for finding barriers although still a little experimental. > It does not give information on the structure optimization using MSR1a. > (PORT is different; for that look up "quasi-Newton optimization".) > > For reference, in some respects MSR1, MSR1a and PORT are AI. They are not > simple. > > -- > Professor Laurence Marks > Department of Materials Science and Engineering, Northwestern University > www.numis.northwestern.edu > "Research is to see what everybody else has seen, and to think what nobody > else has thought" Albert Szent-Györgyi > > On Sun, Jul 3, 2022, 2:59 PM Gavin Abo wrote: > >> Not sure if it helpful or not, but should it be, there was a thread of >> posts related to force minimization back in March of 2021, in it you can >> see it references a "README_Constraints.pdf": >> >> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20952.html >> >> The README_Constraints.pdf appears to be identical to the "Constraint >> structure optimization (pdf)" link which is on the WIEN2k webpage among >> other structure optimization documentation (Structure optimization-notes, >> Notes on the mixer, ...): >> >> http://www.wien2k.at/reg_user/textbooks/ >> >> Kind Regards, >> Gavin >> WIEN2k user >> >> On 7/3/2022 1:26 PM, shamik chakrabarti wrote: >> >> Dear Wien2k users, >> I have a basic question. When the force at >> each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) >> & if the force at each atom is found to be larger than the cut-off values, >> the shifting of atomic coordinates occurs for searching equilibrium. Now, >> here the question arises: >> >> *How did the algorithm know which way to proceed? * >> >> For volume optimization, we fed the data of the lattice parameters & the >> code performs the calculation on the same. But during force minimization, >> we did not feed the values of atomic coordinates apart from the initial >> values, still the code search for new atomic coordinates spontaneously? Is >> it AI? >> >> Looking forward to your reply >> >> with regards, >> >> -- >> Dr. Shamik Chakrabarti >> Research Fellow >> Department of Physics >> Indian Institute of Technology Patna >> Bihta-801103 >> Patna >> Bihar, India >> >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >> > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] A basic question regarding atomic coordinates optimization
You should look at README_10.8, also at http://www.wien2k.at/reg_user/textbooks/README_10.8.pdf Unfortunately the one that Gavin cited is for constrained optimization, which is useful for finding barriers although still a little experimental. It does not give information on the structure optimization using MSR1a. (PORT is different; for that look up "quasi-Newton optimization".) For reference, in some respects MSR1, MSR1a and PORT are AI. They are not simple. -- Professor Laurence Marks Department of Materials Science and Engineering, Northwestern University www.numis.northwestern.edu "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Györgyi On Sun, Jul 3, 2022, 2:59 PM Gavin Abo wrote: > Not sure if it helpful or not, but should it be, there was a thread of > posts related to force minimization back in March of 2021, in it you can > see it references a "README_Constraints.pdf": > > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20952.html > > The README_Constraints.pdf appears to be identical to the "Constraint > structure optimization (pdf)" link which is on the WIEN2k webpage among > other structure optimization documentation (Structure optimization-notes, > Notes on the mixer, ...): > > http://www.wien2k.at/reg_user/textbooks/ > > Kind Regards, > Gavin > WIEN2k user > > On 7/3/2022 1:26 PM, shamik chakrabarti wrote: > > Dear Wien2k users, > I have a basic question. When the force at > each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) > & if the force at each atom is found to be larger than the cut-off values, > the shifting of atomic coordinates occurs for searching equilibrium. Now, > here the question arises: > > *How did the algorithm know which way to proceed? * > > For volume optimization, we fed the data of the lattice parameters & the > code performs the calculation on the same. But during force minimization, > we did not feed the values of atomic coordinates apart from the initial > values, still the code search for new atomic coordinates spontaneously? Is > it AI? > > Looking forward to your reply > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] A basic question regarding atomic coordinates optimization
Not sure if it helpful or not, but should it be, there was a thread of posts related to force minimization back in March of 2021, in it you can see it references a "README_Constraints.pdf": https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20952.html The README_Constraints.pdf appears to be identical to the "Constraint structure optimization (pdf)" link which is on the WIEN2k webpage among other structure optimization documentation (Structure optimization-notes, Notes on the mixer, ...): http://www.wien2k.at/reg_user/textbooks/ Kind Regards, Gavin WIEN2k user On 7/3/2022 1:26 PM, shamik chakrabarti wrote: Dear Wien2k users, I have a basic question. When the force at each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) & if the force at each atom is found to be larger than the cut-off values, the shifting of atomic coordinates occurs for searching equilibrium. Now, here the question arises: *How did the algorithm know which way to proceed? * For volume optimization, we fed the data of the lattice parameters & the code performs the calculation on the same. But during force minimization, we did not feed the values of atomic coordinates apart from the initial values, still the code search for new atomic coordinates spontaneously? Is it AI? Looking forward to your reply with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] A basic question regarding atomic coordinates optimization
Ok, Sir, I will read it. Thank you On Mon, 4 Jul 2022 at 01:09, Laurence Marks wrote: > Please read the documentation that comes with the mixer. > > -- > Professor Laurence Marks > Department of Materials Science and Engineering, Northwestern University > www.numis.northwestern.edu > "Research is to see what everybody else has seen, and to think what nobody > else has thought" Albert Szent-Györgyi > > On Sun, Jul 3, 2022, 2:26 PM shamik chakrabarti > wrote: > >> Dear Wien2k users, >> I have a basic question. When the force at >> each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) >> & if the force at each atom is found to be larger than the cut-off values, >> the shifting of atomic coordinates occurs for searching equilibrium. Now, >> here the question arises: >> >> *How did the algorithm know which way to proceed? * >> >> For volume optimization, we fed the data of the lattice parameters & the >> code performs the calculation on the same. But during force minimization, >> we did not feed the values of atomic coordinates apart from the initial >> values, still the code search for new atomic coordinates spontaneously? Is >> it AI? >> >> Looking forward to your reply >> >> with regards, >> >> -- >> Dr. Shamik Chakrabarti >> Research Fellow >> Department of Physics >> Indian Institute of Technology Patna >> Bihta-801103 >> Patna >> Bihar, India >> ___ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >> > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] A basic question regarding atomic coordinates optimization
Please read the documentation that comes with the mixer. -- Professor Laurence Marks Department of Materials Science and Engineering, Northwestern University www.numis.northwestern.edu "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Györgyi On Sun, Jul 3, 2022, 2:26 PM shamik chakrabarti wrote: > Dear Wien2k users, > I have a basic question. When the force at > each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) > & if the force at each atom is found to be larger than the cut-off values, > the shifting of atomic coordinates occurs for searching equilibrium. Now, > here the question arises: > > *How did the algorithm know which way to proceed? * > > For volume optimization, we fed the data of the lattice parameters & the > code performs the calculation on the same. But during force minimization, > we did not feed the values of atomic coordinates apart from the initial > values, still the code search for new atomic coordinates spontaneously? Is > it AI? > > Looking forward to your reply > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] A basic question regarding atomic coordinates optimization
Dear Wien2k users, I have a basic question. When the force at each atom is calculated & compared with the cut-off values ( ~ 2 mRy/a.u.) & if the force at each atom is found to be larger than the cut-off values, the shifting of atomic coordinates occurs for searching equilibrium. Now, here the question arises: *How did the algorithm know which way to proceed? * For volume optimization, we fed the data of the lattice parameters & the code performs the calculation on the same. But during force minimization, we did not feed the values of atomic coordinates apart from the initial values, still the code search for new atomic coordinates spontaneously? Is it AI? Looking forward to your reply with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
