[Pw_forum] Rydberg to kJ/mole
>Is there any normalisation to be made? Dividing by the number of molecules per unit cell (if there is one per >asymmetric unit, this would refer to 8 for an orthorombic case, e.g.)? QE gives the energy of the cell defined in the input. >I'm not sure, what the "reference" of the calculated Rydberg value is - if it would be the whole cell, I would get >doubled energy values and differences when I calculate a 2x1x1 supercell... Yes. Yo can make the test. there my be a few details. If you double the cell in X direction, divide by 2 the number of k-points in the first direction. If the number of electron is odd, it may be necessary to do a spin polarised calculation. >The other way round: what does "per mole" really mean in a conversion of "some amount" to "a mole" (e.g.: >Joule to Joule/mol)... Take the energy in Ry, multiply by the number of Avogadro, and convert to kJ. My only doubt is per mole o what ? Moles of supercells, molecules or atoms? I do not know. -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120322/091af3e1/attachment.htm
[Pw_forum] Rydberg to KJ/mole
On Mar 22, 2012, at 9:25 , Guntram Schmidt wrote: > Is there any normalisation to be made? energies are given per unit cell. > if it would be the whole cell, I would get doubled energy > values and differences when I calculate a 2x1x1 supercell... you get doubled energy values. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Rydberg to KJ/mole - polymorphs
> My energy differences of 120 and 240 kJ/mole are far too high for > polymorphs (see ?ref [1]). > Am I mistaken to equalize the "total energy" of pwscf-output with the > "lattice energy" (former "structure energy")? > I'm aware of the missing Entropy - but it is told to be negligible > small... I'm not entirely sure I understand your problem; I just want to remind that total energy periodic system does not have any absolute meaning: only energy differences count. So, with what are you comparing the energy of your crystal? As your reference is in kJ/mol your reference could be the homo-atomic molecular phase of the constituents, i.e. O2, N2, H2, and in whetever form C and P are normally bought by a chemistry lab. Another possibility is to compare with isolated atoms, this gives you the binding energy of the crystal. I suspect the details are somewhere in [1]. > I do use nc pseudopotentials and my system is composed of > triphenylphosphine moities with aminobenzoic acids connected. In any case, you MUST use the same pseudopotential and cutoffs when doing the reference calculation for the comparison to be useful. bests -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
[Pw_forum] Rydberg to KJ/mole
Dear Paolo, that's why, I only quoted and argued on energy differences. However, they seem to be too far away from expectation (10-fold). Is there any normalisation to be made? Dividing by the number of molecules per unit cell (if there is one per asymmetric unit, this would refer to 8 for an orthorombic case, e.g.)? I'm not sure, what the "reference" of the calculated Rydberg value is - if it would be the whole cell, I would get doubled energy values and differences when I calculate a 2x1x1 supercell... The other way round: what does "per mole" really mean in a conversion of "some amount" to "a mole" (e.g.: Joule to Joule/mol)... Thanks for helping me! Am 21.03.2012 19:14, schrieb Paolo Giannozzi: > > On Mar 21, 2012, at 17:05 , Alex Kutana wrote: > >> There is a search function for the pw_forum, although It's well hidden > > there are two search functions, both linked and well visible in the > "Contacts" page of the QE web site. > > About the original qeustion: QE calculates total energies per unit cell, > in Ry. The absolute value of the energy depends upon the specific > set of pseudoppotential and has no physical meaning; energy differences > have physical meaning > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > >
[Pw_forum] Rydberg to KJ/mole
On Mar 21, 2012, at 17:05 , Alex Kutana wrote: > There is a search function for the pw_forum, although It's well hidden there are two search functions, both linked and well visible in the "Contacts" page of the QE web site. About the original qeustion: QE calculates total energies per unit cell, in Ry. The absolute value of the energy depends upon the specific set of pseudoppotential and has no physical meaning; energy differences have physical meaning P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Rydberg to KJ/mole - polymorphs
Thanks for the fast reply! This leaves me to the problem of the interpretation of the results. Has anyone experience with the calculation of polymorphic molecular crystals? My energy differences of 120 and 240 kJ/mole are far too high for polymorphs (see ?ref [1]). Am I mistaken to equalize the "total energy" of pwscf-output with the "lattice energy" (former "structure energy")? I'm aware of the missing Entropy - but it is told to be negligible small... I do use nc pseudopotentials and my system is composed of triphenylphosphine moities with aminobenzoic acids connected. I'll attach the input lines [2]. Thanks a lot for further assistance, Guntram [1] Gavezzotti, A., & Filippini, G. (1995). Polymorphic Forms of Organic Crystals at Room Conditions: Thermodynamic and Structural Implications. Journal of the American Chemical Society, 117(49), 12299-12305. doi:10.1021/ja00154a032 [2] calculation = 'scf', restart_mode='from_scratch', prefix='i2t0491.xyz.50.200', tstress = .true., tprnfor = .true., pseudo_dir = '/pseudo/', outdir='/tmp/i2t0491.xyz.50.200/', verbosity = 'high', / ibrav = 14, A = 14.8387, B = 14.8390, C = 18.0441, cosAB = 0, cosAC = 0, cosBC = 0, nat = 392, ntyp = 5, occupations = 'fixed', ecutwfc = 50, ecutrho = 200, input_dft = 'vdW-DF', / conv_thr= 1.0d-8, electron_maxstep= 1000, / ATOMIC_SPECIES P 1.0 P.rpb-nc.UPF O 1.0 O.rpb-nc.UPF N 1.0 N.rpb-nc.UPF H 1.0 H.rpb-nc.UPF C 1.0 C.rpb-nc.UPF ATOMIC_POSITIONS angstrom C 2.8839015.973588 10.295242 . . . K_POINTS automatic 1 1 1 0 0 0 Am 21.03.2012 14:29, schrieb Tone Kokalj: > On Wed, 2012-03-21 at 14:21 +0100, Guntram Schmidt wrote: >> Hello together, >> >> I'm sure, this question has been already asked - but lacking a search >> function for the pw_forum and not having found something using google, >> I'm urged to ask this question to the list: >> >> How do I convert the output of pwscf (which is in Ry) to kJ per mole? > > ? > -- > > 1.0 ry = > = 0.5 hartree > = 1.0 ry > = 13.605691930242388 eV > = 1312.7496997450642 kJ/mol > = 313.75470835207074 kcal/mol > = 2.17987197e-21 kJ > = 5.21001904875717e-22 kcal > = 2.179871970002e-11 erg > > As a convenience you may use the "unitconv" utility of xcrysden > (attached). > > Regards, Tone > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Rydberg to KJ/mole
On Wed, 2012-03-21 at 14:21 +0100, Guntram Schmidt wrote: > Hello together, > > I'm sure, this question has been already asked - but lacking a search > function for the pw_forum and not having found something using google, > I'm urged to ask this question to the list: > > How do I convert the output of pwscf (which is in Ry) to kJ per mole? ? -- 1.0 ry = = 0.5 hartree = 1.0 ry = 13.605691930242388 eV = 1312.7496997450642 kJ/mol = 313.75470835207074 kcal/mol = 2.17987197e-21 kJ = 5.21001904875717e-22 kcal = 2.179871970002e-11 erg As a convenience you may use the "unitconv" utility of xcrysden (attached). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- A non-text attachment was scrubbed... Name: unitconv Type: application/x-shellscript Size: 2488 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120321/c286fe31/attachment.bin
[Pw_forum] Rydberg to KJ/mole
Hello together, I'm sure, this question has been already asked - but lacking a search function for the pw_forum and not having found something using google, I'm urged to ask this question to the list: How do I convert the output of pwscf (which is in Ry) to kJ per mole? Conversion to Joules seems to be not a question, using pen or some tools (e.g., http://www.chemie.fu-berlin.de/chemistry/general/units_en.html). Do I have to multiply the outcome with the avogadro number to get KJ/mol? If so, I'm wondering about the outcome of my calculations. I have two sets of two polymorphic molecular crystals. The have energy differences of 0.09492046 Ry and 0.21669732 Ry, resp. . This would correspond to ca. 120 and 280 kJ/mole! This would exceed the expected energy differences of polymorphs (10-25 kJ/mole) by one order of magnitude! Did I miss something? Has there some other normalisation to be made? Thanks a lot for help, Guntram
[Pw_forum] Rydberg to KJ/mole
On Wed, Mar 21, 2012 at 9:21 AM, Guntram Schmidt < guntram.schmidt at chemie.uni-halle.de> wrote: > Hello together, > > I'm sure, this question has been already asked - but lacking a search > function for the pw_forum > There is a search function for the pw_forum, although It's well hidden. Here is the URL: http://www.google.com/cse/home?cx=000217952118062629757:xew9tb5yarq Alex -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120321/6f98d051/attachment.htm
