[Wien] DFT-D3 Forces
I found in a 2014 mail that there was a problem with the dftd3 executable for the computation of forces. Does anyone know if this problem was solved with the last release of the dftd3 package? Thanks, Bruno ___ 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] SCF and symmetry
I'm studying a molecular crystal in which two different molecules form an 1:1 adduct. There are 2 molecules of each kind (4 in total) in the unit cell. There are 19 atoms in the asymmetric unit, and since it belongs to the P21/c spacegroup, a total of 76 atoms are contained in the unit cell. I was trying to find a possible mistake when calculating interaction energies and I found the next problem: If I calculate the SCF by manually inserting the 76 positions and giving it a P1 symmetry the energy converged to-5752.17735109 Ry. If I calculate the SCF by inserting the 19 atoms of the asymmetric unit with the correct symmetry and let the program to generate the rest of the positions (which where exactly the same as when inserted manually), the same functional, same RMT, same K points and same convergence criteria the energy converged to-5752.17735109 Ry. Transforming the energy difference between the 2 calculations gives 195 kcal/mol. The same happened when doing the same for other systems. My question is, ¿shouldn't I get the same energy in both calculations since it's the same system, same coordinates and the input was prepared equally except for the symmetry? Since I'm trying to calculate interaction energies using different subsystems, some with and some without symmetry, this is a relevant question to my research. Greetings, Bruno L ___ 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] SCF and symmetry
Dear Laurence Marks: Yes, I'm sorry. First energy is: -5752.55335845 Ry Second energy is -5752.17735109 Ry Enviado desde Correo de Windows De: Laurence Marks Enviado el: lunes, 30 de noviembre de 2015 09:06 p. m. Para: wien@zeus.theochem.tuwien.ac.at Typos in your energies? On Mon, Nov 30, 2015 at 8:00 PM, Bruno Landeros <brunolande...@hotmail.com> wrote: I'm studying a molecular crystal in which two different molecules form an 1:1 adduct. There are 2 molecules of each kind (4 in total) in the unit cell. There are 19 atoms in the asymmetric unit, and since it belongs to the P21/c spacegroup, a total of 76 atoms are contained in the unit cell. I was trying to find a possible mistake when calculating interaction energies and I found the next problem: If I calculate the SCF by manually inserting the 76 positions and giving it a P1 symmetry the energy converged to -5752.17735109 Ry. If I calculate the SCF by inserting the 19 atoms of the asymmetric unit with the correct symmetry and let the program to generate the rest of the positions (which where exactly the same as when inserted manually), the same functional, same RMT, same K points and same convergence criteria the energy converged to -5752.17735109 Ry. Transforming the energy difference between the 2 calculations gives 195 kcal/mol. The same happened when doing the same for other systems. My question is, ¿shouldn't I get the same energy in both calculations since it's the same system, same coordinates and the input was prepared equally except for the symmetry? Since I'm trying to calculate interaction energies using different subsystems, some with and some without symmetry, this is a relevant question to my research. Greetings, Bruno L -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi___ 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] SCF and symmetry
The first time I generated the Nosymm structure file was by using the 76 posiciones generated by a first symmetric scf calculation (no coordinate optimization), so the same coordinates where used in both cases. To be sure, I run again the Nosymm structure file but accepted the new structfile suggested by the SGROUP program, which detected the corrected symmetry and this gave the energy I just mentioned here, so in principle they are equivalent. Would you like me to send you the case.struct files with the specifications I gave with init_lapw? Enviado desde Correo de Windows De: pbl...@theochem.tuwien.ac.at Enviado el: martes, 1 de diciembre de 2015 12:53 a. m. Para: wien@zeus.theochem.tuwien.ac.at No. This is a huge E-difference which must come from something very severe. Did you compare the distances in the 2 case.outputnn file or compare the structures in xcrysden. On 12/01/2015 07:37 AM, Bruno Landeros wrote: > Dear Peter: > > Yes, my mistake. First energy (no symmetry) is > -5752.55335845 Ry. > while second energy is > -5752.17735109 Ry. > > Since cell parameters are note small (12.994513, 25.002400, 17.381701 Bohr) > and I was testing convergence I asked for just 1 K point in both cases. > May be this the origin of the discrepancy? > > Greetings, > > Bruno > > > Enviado desde Correo de Windows > > *De:* pbl...@theochem.tuwien.ac.at <mailto:pbl...@theochem.tuwien.ac.at> > *Enviado el:* martes, 1 de diciembre de 2015 12:16 a. m. > *Para:* wien@zeus.theochem.tuwien.ac.at > <mailto:wien@zeus.theochem.tuwien.ac.at> > > The energies you posted are identical ! > > Anyway: I hope you did not just copy the case.klist file from the low to > the high-symmetry case ?? > > Otherwise: send me your 2 struct files together with the description of > the chosen calculational parameters (everything which is non-default) to > my private email. > > Am 01.12.2015 um 03:00 schrieb Bruno Landeros: > > I'm studying a molecular crystal in which two different molecules form > > an 1:1 adduct. There are 2 molecules of each kind (4 in total) in the > > unit cell. There are 19 atoms in the asymmetric unit, and since it > > belongs to the P21/c spacegroup, a total of 76 atoms are contained in > > the unit cell. I was trying to find a possible mistake when calculating > > interaction energies and I found the next problem: > > > > If I calculate the SCF by manually inserting the 76 positions and giving > > it a P1 symmetry the energy converged to > > -5752.17735109 Ry. > > > > If I calculate the SCF by inserting the 19 atoms of the asymmetric unit > > with the correct symmetry and let the program to generate the rest of > > the positions (which where exactly the same as when inserted manually), > > the same functional, same RMT, same K points and same convergence > > criteria the energy converged to > > -5752.17735109 Ry. > > > > Transforming the energy difference between the 2 calculations gives 195 > > kcal/mol. The same happened when doing the same for other systems. > > > > My question is, ¿shouldn't I get the same energy in both calculations > > since it's the same system, same coordinates and the input was prepared > > equally except for the symmetry? > > Since I'm trying to calculate interaction energies using different > > subsystems, some with and some without symmetry, this is a relevant > > question to my research. > > > > > > Greetings, > > > > Bruno L > > > > > > ___ > > 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 > <http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/index.html> > > > > -- > -- > Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna > Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 > Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at > WWW: http://www.imc.tuwien.ac.at/staff/tc_group_e.php > -- > ___ > 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.ht
Re: [Wien] Structure Factors
Dear Peter At the end of the file there is a table with the structure factors but I would like to understand how to get this from the atomic contributions that come at the beggining of the output3 file. Thanks To: wien@zeus.theochem.tuwien.ac.at From: pbl...@theochem.tuwien.ac.at Date: Sat, 31 Oct 2015 17:45:14 +0100 Subject: Re: [Wien] Structure Factors lapw3 calculates static X-ray structure factors, so they can be directly compared to the experimental ones. PS: Often, it gives better agreement, when you just take the valence structrure factors and add the core strucutre factors from atomic HF-theory (after all, this is how experimental structure factors are refined). Am 30.10.2015 um 22:40 schrieb Bruno Landeros: Dear all: How can I transform the data obtained from a lapw3 calculation in order to compare the DFT theoretical structure factors with the experimental (static) ones? Thanks in advance, Bruno L ___ 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 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] Structure Factors
Thank you, this was what I was looking for. Greetings Enviado desde mi iPhone > El 31/10/2015, a las 1:42 p.m., Peter Blaha <pbl...@theochem.tuwien.ac.at> > escribió: > > It first lists all the (nonspherical) contributions of all atomic spheres, > than of the interstital and further down you can find the total structure > factors. > >> Am 31.10.2015 um 18:09 schrieb Bruno Landeros: >> Dear Blaha: >> >> Thank you for the tip about the valence structure factors. >> >> Still I am confused. For each HKL in the output file I have about 50 >> contributions per atom. Is there an equation to transform all this data into >> a single F value for each HKL in order to compare to the experiment? >> >> Thanks in advance >> >> Enviado desde mi iPhone >> >> El 31/10/2015, a las 10:45 a.m., Peter Blaha <pbl...@theochem.tuwien.ac.at> >> escribió: >> >>> lapw3 calculates static X-ray structure factors, so they can be directly >>> compared to the experimental ones. >>> >>> PS: Often, it gives better agreement, when you just take the valence >>> structrure factors and add the core strucutre factors from atomic HF-theory >>> (after all, this is how experimental structure factors are refined). >>> >>> >>>> Am 30.10.2015 um 22:40 schrieb Bruno Landeros: >>>> Dear all: >>>> >>>> How can I transform the data obtained from a lapw3 calculation in order to >>>> compare the DFT theoretical structure factors with the experimental >>>> (static) ones? >>>> >>>> Thanks in advance, >>>> >>>> Bruno L >>>> >>>> >>>> ___ >>>> 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 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 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] Problem with aim.def
Dese Gabin: I didn't craeate manually the aim.def. First I tried by using $ x aim Then it was automatically generated but giving the same mistake. Then I tried: $ x aim -d To generate the aim.def and then run ir. But the mistake was the same in either case: ERROR IN OPENING AIM.DEF AIM.DEF Thank you for answering! Have you another suggestion of what may be possibly wrong? Greetings Bruno Enviado desde mi iPhone > El 18/09/2015, a las 13:59, Gavin Abo <gs...@crimson.ua.edu> escribió: > > If $ is the bash terminal. > > It seems like you might have just did (while in the case directory): > > $ aim > > However, if you see the WIEN2k 14.2 usersguide on page 134 in section "8.1.1 > Execution" [ http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ]. The > command needs to be: > > $ x aim > > or > > Real: $ aim aim.def > Complex: $ aimc aim.def > > "x aim" should automatically create aim.def. Since you manually created > aim.def, I assume that you are using "aim[c] aim.def". So check if the name > of the file in the directory (aim.def) and command (aim aim.def) are > consistent. In Linux, case sensitivity can be important. For example, > aim.def (with lowercase letters) and AIM.DEF (with uppercase letters) are > considered different. > >> On 9/18/2015 11:25 AM, Bruno Landeros wrote: >> Dear users: >> >> I'm having trouble when I try to run the aim module. >> >> I have already created the aim.def file which looks like this >> >> 5 ,'hpn_final_converged.inaim', 'old','formatted',0 >> 6 ,'hpn_final_converged.outputaim', 'unknown','formatted',0 >> 8 ,'hpn_final_converged.struct','old','formatted',0 >> 9 ,'hpn_final_converged.clmsum','old','formatted',0 >> 21,'hpn_final_converged.surf', 'unknown','formatted',0 >> 22,'hpn_final_converged.crit', 'unknown','formatted',0 >> 77,'hpn_final_converged.aim_surface_errors', 'unknown','formatted',0 >> >> But when I execute the program I get always the same error: >> >> >> >> ERROR IN OPENING AIM.DEF !!! >> >> AIM.DEF >> >> >> The three files needed hpn_final_converged.struct, >> hpn_final_converged.clmsum and hpn_final_converged.inaim are present. >> For the last one I'm using the same as the manual's example: >> >> CRIT >> 1 >> ALL >> 3 3 3 >> END >> >> What can possibly be wrong? >> >> >> Thanks in advance, >> >> Bruno L > ___ > 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] Problem with aim.def
Dear Gavin: I was trying to run inside a subdirectory created by the save_lawp -d option. This subdirectory was /home/bruno/Wien2k/hpn_final/hpn_final_converged. I tried to run in a previous directory which is /home/bruno/Wien2k/hpn_final and it finally worked. Maybe something was wrong with the full path of the subdirectory. Thank you very much! To: wien@zeus.theochem.tuwien.ac.at From: gs...@crimson.ua.edu Date: Fri, 18 Sep 2015 16:24:59 -0600 Subject: Re: [Wien] Problem with aim.def I do a quick test in a bash ($) terminal and this is what I get: username@computername:~/Desktop/test$ pwd /home/username/Desktop/test <= What is your full path? If it is long, try shorting it. Is your directory name "hpn_final_converged" or this the name cutoff? username@computername:~/Desktop/test$ rm aim.def <= Maybe, remove the aim.def and try again. username@computername:~/Desktop/test$ aim ERROR IN OPENING AIM.DEF AIM.DEF username@computername:~/Desktop/test$ aim aim.def ERROR IN OPENING AIM.DEF AIM.DEF username@computername:~/Desktop/test$ ls -l aim.def ls: cannot access aim.def: No such file or directory username@computername:~/Desktop/test$ x aim 1.0u 0.0s 0:01.02 99.0% 0+0k 0+96io 0pf+0w <= I experience no error here with "x aim". username@computername:~/Desktop/test$ ls -l aim.def -rw-rw-r-- 1 username username 330 Sep 18 16:04 aim.def <= What are your read permissions for aim.def? username@computername:~/Desktop/test$ cat aim.def 5 ,'test.inaim', 'old','formatted',0 6 ,'test.outputaim', 'unknown','formatted',0 8 ,'test.struct','old','formatted',0 9 ,'test.clmsum','old','formatted',0 21,'test.surf', 'unknown','formatted',0 22,'test.crit', 'unknown','formatted',0 77,'test.aim_surface_errors', 'unknown','formatted',0 On 9/18/2015 1:28 PM, Bruno Landeros wrote: Dese Gabin: I didn't craeate manually the aim.def. First I tried by using $ x aim Then it was automatically generated but giving the same mistake. Then I tried: $ x aim -d To generate the aim.def and then run ir. But the mistake was the same in either case: ERROR IN OPENING AIM.DEF AIM.DEF Thank you for answering! Have you another suggestion of what may be possibly wrong? Greetings Bruno ___ 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
