https://www.vasp.at/wiki/api.php?action=feedcontributions&user=Doris&feedformat=atomVASP Wiki - User contributions [en]2024-03-29T11:42:39ZUser contributionsMediaWiki 1.40.1https://www.vasp.at/wiki/index.php?title=CO_vibration&diff=6095CO vibration2018-10-24T16:06:21Z<p>Doris: </p>
<hr />
<div>{{Template:At_and_mol}}<br />
<br />
== Task ==<br />
<br />
Calculation of the vibrational frequencies of a CO molecule.<br />
<br />
== Input ==<br />
<br />
=== {{TAG|POSCAR}} ===<br />
CO molecule in a box<br />
1.0 ! universal scaling parameters<br />
8.0 0.0 0.0 ! lattice vector a(1)<br />
0.0 8.0 0.0 ! lattice vector a(2)<br />
0.0 0.0 8.0 ! lattice vector a(3)<br />
1 1 ! number of atoms for each species<br />
sel ! selective degrees of freedom are changed<br />
cart ! positions in cartesian coordinates<br />
0 0 0 F F T ! first atom<br />
0 0 1.143 F F T ! second atom<br />
<br />
Alternatively, try to fix one of the atoms completely.<br />
<br />
=== {{TAG|INCAR}} ===<br />
{{TAGBL|SYSTEM}} = CO molecule in a box<br />
{{TAGBL|ISMEAR}} = 0 ! Gaussian smearing<br />
{{TAGBL|IBRION}} = 5 ! use the conjugate gradient algorithm<br />
{{TAGBL|NFREE}} = 2 ! central differences<br />
{{TAGBL|POTIM}} = 0.02 ! 0.02 A stepwidth <br />
{{TAGBL|NSW}} = 1 ! ionic steps > 0<br />
<br />
=== {{FILE|KPOINTS}} ===<br />
Gamma-point only<br />
0<br />
Monkhorst Pack<br />
1 1 1<br />
0 0 0<br />
<br />
== Calculation ==<br />
<br />
*The selected degrees of freedom are displaced once in the direction <math>\hat{x}</math> and once in <math>-\hat{x}</math> by 0.02 <math>\AA</math> ({{TAG|POTIM}}). <br />
<br />
*In the present case this makes 4 displacements plus the equilibrium positions (i.e. a total of five ionic configurations).<br />
<br />
=== {{TAG|OUTCAR}} ===<br />
<br />
At the end of the {{TAG|OUTCAR}} file the following output should be obtained:<br />
<br />
SECOND DERIVATIVES (NOT SYMMETRIZED)<br />
------------------------------------<br />
1Z 2Z<br />
1Z -114.737304 114.737304<br />
2Z 114.458316 -114.458316<br />
<br />
<br />
Eigenvectors and eigenvalues of the dynamical matrix<br />
----------------------------------------------------<br />
<br />
<br />
1 f = 63.887522 THz 401.417139 2PiTHz 2131.058277 cm-1 264.217647 meV<br />
X Y Z dx dy dz<br />
0.000000 0.000000 0.000000 0 0 -0.655280<br />
0.000000 0.000000 1.143000 0 0 0.755386<br />
<br />
2 f/i= 0.038494 THz 0.241864 2PiTHz 1.284016 cm-1 0.159198 meV<br />
X Y Z dx dy dz<br />
0.000000 0.000000 0.000000 0 0 -0.755386<br />
0.000000 0.000000 1.143000 0 0 -0.655280<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/COvib.tgz COvib.tgz]<br />
<br />
{{Template:At_and_mol}}<br />
<br />
Back to the [[The_VASP_Manual|main page]].<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=DOSCAR&diff=6065DOSCAR2018-09-04T10:13:17Z<p>Doris: </p>
<hr />
<div>The {{TAG|DOSCAR}} file contains the DOS and integrated DOS. The units are number of states/eV and number of states, respectively and thus extensively defined. The intensive DOS is obtained by dividing by the Volume of the unit cell. ''For dynamic simulations and relaxations, an averaged DOS and an averaged integrated DOS is written to the file. For a description of how the averaging is done see the tags {{TAG|NBLOCK}}, {{TAG|KBLOCK}}, {{TAG|EMIN}}, {{TAG|EMAX}} and {{TAG|NEDOS}}. The first few lines of the {{TAG|DOSCAR}} file are made up by a header:<br />
<br />
Number of Ions (including empty spheres), Number of Ions, 0 (no partial DOS) or 1 (incl. partial DOS), NCDIJ (currently not used) <br />
Volume of the unit cell [Angst**3], length of the basis vectors (a,b,c [m]), {{TAG|POTIM}}[s]<br />
the initial Temperature {{TAG|TEBEG}} <br />
'CAR'<br />
the name of the system as given by {{TAG|SYSTEM}} in {{TAG|INCAR}}<br />
E(max), E(min), (the energy range in which the DOS is given), {{TAG|NEDOS}}, E(fermi), 1.0000<br />
<br />
which is followed by {{TAG|NEDOS}} lines holding three data<br />
<br />
energy DOS integrated DOS<br />
<br />
The density of states (DOS) <math>\bar n</math>, is actually determined as the difference of the integrated DOS between two pins, i.e.<br />
<br />
<math> \bar n(\epsilon_i) = (N(\epsilon_i) - N(\epsilon_{i-1})) / \Delta \epsilon </math><br />
<br />
where <math>\Delta \epsilon</math> is the distance between two pins (energy difference between two grid point in the {{TAG|DOSCAR}} file), and <math>N(\epsilon_i)</math> is the integrated DOS<br />
<br />
<math>N (\epsilon_{i}) = \int_{-\infty}^{\epsilon_i} n(\epsilon) d \epsilon.</math><br />
<br />
This method conserves the total number of electrons exactly. For spin-polarized calculations each line holds five data<br />
<br />
energy DOS(up) DOS(dwn) integrated DOS(up) integrated DOS(dwn)<br />
<br />
If {{TAG|RWIGS}} or {{TAG|LORBIT}} (important for Wigner Seitz radii) is set in the {{TAG|INCAR}} file, an lm- and site-projected DOS isvcalculated and also written to the {{TAG|DOSCAR}} file. One set of data is written for each ion, each set of data holds {{TAG|NEDOS}} lines with the following data<br />
<br />
l-resolved:<br />
energy s-DOS p-DOS d-DOS,<br />
<br />
lm-resolved DOS (l,-m,...,l,0,...l-,+m):<br />
energy, <math> s, p_y, p_z, p_x, d_{xy}, d_{yz}, d_{z2-r2}, d_{xz}, d_{x2-y2},...</math><br />
<br />
for spin-polarized systems {{TAG|ISPIN = 2}}:<br />
<br />
energy s-DOS(up) s-DOS(down) p-DOS(up) p-DOS(dwn) d-DOS(up) d-DOS(dwn)<br />
<br />
for the non spin-polarized and spin polarized case respectively. As before the written densities are understood as the difference of the integrated DOS between two pins.<br />
<br />
For non-collinear calculations, the total DOS has the following format:<br />
<br />
energy DOS(total) integrated-DOS(total) <br />
<br />
Information on the individual spin components is available only for the site projected density of states, which has the format:<br />
<br />
energy s-DOS(total) s-DOS(mx) s-DOS(my) s-DOS(mz) p-DOS(total) p-DOS(mx) ...<br />
<br />
In this case, the (site projected) total density of states (total) and the (site projected) energy resolved magnetization density in the <math>x</math> (mx), <math>y</math> (my) and <math>z</math> (mz) directions are available.<br />
<br />
In all cases, the units of the l- and site projected DOS are states/atom/energy.<br />
<br />
The site projected DOS is not evaluated in the parallel version for the following cases:<br />
*vasp.4.5, {{TAG|NPAR}}<math>\ne</math>1 no site projected DOS <br />
*vasp.4.6, {{TAG|NPAR}}<math>\ne</math>1, {{TAG|LORBIT}}=0-5 no site projected DOS <br />
In vasp.4.6 the site projected DOS can be evaluated for {{TAG|LORBIT}}=10-12, even if {{TAG|NPAR}} is not equal 1 (contrary to previous releases).<br />
*vasp.5 needs no specification of {{TAG|NPAR}} <br />
<br />
Mind: For relaxations, the {{TAG|DOSCAR}} is usually useless. If you want to get an accurate DOS for the final configuration, first copy {{TAG|CONTCAR}} to {{TAG|POSCAR}} and continue with one static ({{TAG|ISTART}}=1; {{TAG|NSW}}=0) calculation.<br />
<br />
----<br />
<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:Files]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=GGA&diff=4196GGA2017-05-02T10:29:32Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|GGA|91 {{!}} PE {{!}} RP {{!}} PS {{!}} AM| type of exchange-correlation in accordance with the {{FILE|POTCAR}} file}}<br />
<br />
Description: {{TAG|GGA}} specifies the type of generalized-gradient-approximation one wishes to use.<br />
----<br />
This tag was added to perform GGA calculation with pseudopotentials generated with conventional LDA reference configurations.<br />
<br />
Possible options are:<br />
<br />
:{| border="1" cellspacing="0" cellpadding="5"<br />
<!-- these first three options have been obsolete since VASP.4.X<br />
|PB || Perdew - Becke<br />
|-<br />
|PW || Perdew - Wang 86<br />
|-<br />
|LM || Langreth-Mehl-Hu<br />
|- --><br />
|{{TAG|GGA}} || Description<br />
|-<br />
|91 || Perdew - Wang 91<ref name="perdew1992"/><br />
|-<br />
|PE || Perdew-Burke-Ernzerhof<ref name="perdew1996"/><br />
|-<br />
|AM || AM05<ref name="armiento:prb:05"/><ref name="mattson:jcp:08"/><ref name="mattson:prb:09"/><br />
|-<br />
|HL || Hendin-Lundqvist<ref name="hedin1971"/><br />
|-<br />
|CA || Ceperley-Alder<ref name="ceperley1980"/><br />
|-<br />
|PZ || Ceperley-Alder, parametrization of Perdew-Zunger<ref name="perdewzunger1981"/><br />
|-<br />
|WI || Wigner<ref name="wigner1937"/><br />
|-<br />
|RP || revised Perdew-Burke-Ernzerhof (RPBE)<ref name="hammer1999"/> with Pade Approximation<br />
|-<br />
|VW || Vosko-Wilk-Nusair<ref name="vokso1980"/> (VWN)<br />
|-<br />
|B3 || B3LYP<ref name="b3lyp"/> (Joachim Paier), where LDA part is with VWN3-correlation<br />
|-<br />
|B5 || B3LYP (Joachim Paier), where LDA part is with VWN5-correlation<br />
|-<br />
|BF || BEEF<ref name="beef2012"/>, xc (with libbeef)<br />
|-<br />
|CO || no exchange-correlation<br />
|-<br />
|PS || Perdew-Burke-Ernzerhof revised for solids (PBEsol)<ref name="perdew:prl:08"/><br />
|-<br />
|for range-separated ACFDT: ||<br />
|-<br />
|RA || new RPA Perdew Wang (by Judith Harl)<br />
|-<br />
|03 || range-separated ACFDT (LDA - sr RPA) <math>\mu=0.3 \AA^3</math> <br />
|-<br />
|05 || range-separated ACFDT (LDA - sr RPA) <math>\mu=0.5 \AA^3</math><br />
|-<br />
|10 || range-separated ACFDT (LDA - sr RPA) <math>\mu=1.0 \AA^3</math> <br />
|-<br />
|20 || range-separated ACFDT (LDA - sr RPA) <math>\mu=2.0 \AA^3</math><br />
|-<br />
|PL || new RPA+ Perdew Wang (by Judith Harl)<br />
|-<br />
|for vdW (Jiri Klimes): ||<br />
|-<br />
|RE || revPBE<ref name="zhang1998"/><br />
|-<br />
|OR || optPBE<ref name="klimes2010"/><br />
|-<br />
|BO || optB88<ref name="klimes2010"/><br />
|-<br />
|MK || optB86b<ref name="klimes2010"/><br />
|}<br />
<br />
The tags AM (AM05) and PS (PBEsol) are only supported by VASP.5.X. The AM05 functional and the PBEsol functional are constructed using different principles, but both aim at a decent description of yellium surface energies. In practice, they yield quite similar results for most materials. Both are available for spin polarized calculations.<br />
<br />
{{sc|GGA|Examples|Examples that use this tag}}<br />
<br />
== References ==<br />
<references><br />
<ref name="armiento:prb:05">[http://link.aps.org/doi/10.1103/PhysRevB.72.085108 R. Armiento and A. E. Mattsson, Phys. Rev. B 72, 085108 (2005).]</ref><br />
<ref name="mattson:jcp:08">[http://dx.doi.org/10.1063/1.2835596 A. E. Mattsson, R. Armiento, J. Paier, G. Kresse, J.M. Wills, and T.R. Mattsson, J. Chem. Phys. 128, 084714 (2008).]</ref><br />
<ref name="mattson:prb:09">[http://link.aps.org/doi/10.1103/PhysRevB.79.155101 A. E. Mattsson and R. Armiento, Phys. Rev. B 79, 155101 (2009).]</ref><br />
<ref name="perdew:prl:08">[http://link.aps.org/doi/10.1103/PhysRevB.79.155107 J. P. Perdew, A. Ruzsinszky, G. I. Csonka, O. A. Vydrov, G. E. Scuseria, L. A. Constantin, X. Zhou, and K. Burke, Phys. Rev. Lett. 100, 136406 (2008).]</ref><br />
<ref name="hedin1971">[http://iopscience.iop.org/article/10.1088/0022-3719/4/14/022/meta;jsessionid=6F1B9F8BE588208D706AAD78E6F0E49A.c2.iopscience.cld.iop.org L. Hedin and B. I. Lundqvist, J. Phys. C 4, 2064 (1971).]</ref><br />
<ref name="ceperley1980">[http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.45.566 D. M. Ceperley and B. J. Alder, Phys. Rev. Lett. 45, 566 (1980).]</ref><br />
<ref name="perdewzunger1981">[http://journals.aps.org/prb/abstract/10.1103/PhysRevB.23.5048 J. P. Perdew and Alex Zunger, Phys. Rev. B 23, 5048 (1981).]</ref><br />
<ref name="wigner1937">[http://aip.scitation.org/doi/10.1063/1.1750108 E. Wigner, J. Chem. Phys. 5, 726 (1937).]</ref><br />
<ref name="hammer1999">[http://journals.aps.org/prb/abstract/10.1103/PhysRevB.59.7413 B. Hammer, L. B. Hansen and J. K. Nørskov, Phys. Rev. B 59, 7413 (1999).]</ref><br />
<ref name="vokso1980">[http://www.nrcresearchpress.com/doi/abs/10.1139/p80-159#.WJLvYmf950w S. H. Vosko, L. Wilk and M. Nusair, Can. J. Phys. 58, 1200 (1980).]</ref><br />
<ref name="b3lyp">[http://aip.scitation.org/doi/10.1063/1.464913 A. D. Becke, J. Chem. Phys. 98, 5648 (1993).]</ref><br />
<ref name="beef2012">[http://journals.aps.org/prb/abstract/10.1103/PhysRevB.85.235149 Jess Wellendorff, Keld T. Lundgaard, Andreas Møgelhøj, Vivien Petzold, David D. Landis, Jens K. Nørskov, Thomas Bligaard and Karsten W. Jacobsen, Phys. Rev. B 85, 235149 (2012).]</ref><br />
<ref name="zhang1998">[http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.80.890 Y. Zhang and W. Yang, Phys. Rev. Lett. 80, 890 (1998).]</ref><br />
<ref name="klimes2010">[http://iopscience.iop.org/article/10.1088/0953-8984/22/2/022201/meta J. Klimeš, D. R. Bowler, and A. Michaelides, J. Phys.: Cond. Matt. 22, 022201 (2010).]</ref><br />
<ref name="perdew1992">[http://journals.aps.org/prb/abstract/10.1103/PhysRevB.45.13244 J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992).]</ref><br />
<ref name="perdew1996">[http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.77.3865 J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).]</ref><br />
</references><br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2372ICAMM Rennes 20162016-08-30T11:55:27Z<p>Doris: /* Lectures */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics1.pdf DFT, PW, and PAW]: "VASP: The basics(1). DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics2.pdf electronic convergence, BZ sampling]: "VASP: The basics(2). electronic convergence, BZ sampling ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics3.pdf structure relaxation, MD]: "VASP: The basics(3). structure relaxation, phonons, MD...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Dielectric.pdf Dielectric properties]: "VASP: Dielectric response. Perturbation theory, linear response, and finite electric fields".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_BSE.pdf BSE]: "VASP: Beyond DFT. The Bethe-Salpeter Equation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_from_atoms_to_bulk.pdf From Atoms to Bulk systems]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_surface_science.pdf Surface Science]: A description of the examples "A bit of surface science".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_ammonia_flipping.pdf Ammonia Flipping]: A description of the examples "Transition State Search methods".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_h2o_on_tio2.pdf Adsorption of H2O on TiO2]: A description of the examples "Constrained Molecular Dynamics".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_dielectrics_and_RPA.pdf Dielectric properties and RPA]: A description of the examples "Dielectric properties and RPA".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Hybrid functionals ===<br />
<br />
[[bandgap of Si using different DFT+HF methods]]<br />
<br />
[[fcc Ni DOS with hybrid functional]]<br />
<br />
[[Si HSE bandstructure]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Adsorption of H2O on TiO2 using standard relaxation and constrained MD ===<br />
<br />
[[standard relaxation]]<br />
<br />
[[constrained MD using a canonical ensemble]]<br />
<br />
[[ constrained MD using a microcanonical ensemble]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
=== Dielectric properties and RPA ===<br />
<br />
[[dielectric properties of SiC]]<br />
<br />
[[bandgap of Si in GW]]<br />
<br />
[[equilibrium volume of Si in the RPA]]<br />
<br />
[[bandstructure of SrVO3 in GW]]<br />
<br />
[[dielectric properties of Si using BSE]]<br />
<br />
[[model BSE calculation on Si]]<br />
<br />
=== NMR calculations ===<br />
<br />
[[alpha-SiO2]]<br />
<br />
[[alpha-AlF3]]<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Constrained_MD_using_a_microcanonical_ensemble&diff=2362Constrained MD using a microcanonical ensemble2016-08-29T13:55:53Z<p>Doris: Created page with "== Download == [http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder constrMD_microcanonical] ---- VASP_example_calculations|To the list of..."</p>
<hr />
<div>== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder constrMD_microcanonical]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Constrained_MD_using_a_canonical_ensemble&diff=2361Constrained MD using a canonical ensemble2016-08-29T13:55:15Z<p>Doris: Created page with "== Download == [http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder constrMD_canonical] ---- VASP_example_calculations|To the list of exam..."</p>
<hr />
<div>== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder constrMD_canonical]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Standard_relaxation&diff=2360Standard relaxation2016-08-29T13:54:16Z<p>Doris: Created page with "== Download == [http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder std_relaxation] ---- VASP_example_calculations|To the list of examples..."</p>
<hr />
<div>== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/h2o_on_tio2.tgz h2o_on_tio2.tgz, sub-folder std_relaxation]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2359ICAMM Rennes 20162016-08-29T13:47:09Z<p>Doris: /* Exercises */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics1.pdf DFT, PW, and PAW]: "VASP: The basics(1). DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics2.pdf electronic convergence, BZ sampling]: "VASP: The basics(2). electronic convergence, BZ sampling ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics3.pdf structure relaxation, MD]: "VASP: The basics(3). structure relaxation, phonons, MD...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Dielectric.pdf Dielectric properties]: "VASP: Dielectric response. Perturbation theory, linear response, and finite electric fields".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_from_atoms_to_bulk.pdf From Atoms to Bulk systems]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_surface_science.pdf Surface Science]: A description of the examples "A bit of surface science".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_ammonia_flipping.pdf Ammonia Flipping]: A description of the examples "Transition State Search methods".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_h2o_on_tio2.pdf Adsorption of H2O on TiO2]: A description of the examples "Constrained Molecular Dynamics".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_dielectrics_and_RPA.pdf Dielectric properties and RPA]: A description of the examples "Dielectric properties and RPA".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Hybrid functionals ===<br />
<br />
[[bandgap of Si using different DFT+HF methods]]<br />
<br />
[[fcc Ni DOS with hybrid functional]]<br />
<br />
[[Si HSE bandstructure]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Adsorption of H2O on TiO2 using standard relaxation and constrained MD ===<br />
<br />
[[standard relaxation]]<br />
<br />
[[constrained MD using a canonical ensemble]]<br />
<br />
[[ constrained MD using a microcanonical ensemble]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
=== Dielectric properties and RPA ===<br />
<br />
[[dielectric properties of SiC]]<br />
<br />
[[bandgap of Si in GW]]<br />
<br />
[[equilibrium volume of Si in the RPA]]<br />
<br />
[[bandstructure of SrVO3 in GW]]<br />
<br />
[[dielectric properties of Si using BSE]]<br />
<br />
[[model BSE calculation on Si]]<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2354ICAMM Rennes 20162016-08-29T13:28:57Z<p>Doris: /* Tutorials */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics1.pdf DFT, PW, and PAW]: "VASP: The basics(1). DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics2.pdf electronic convergence, BZ sampling]: "VASP: The basics(2). electronic convergence, BZ sampling ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics3.pdf structure relaxation, MD]: "VASP: The basics(3). structure relaxation, phonons, MD...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Dielectric.pdf Dielectric properties]: "VASP: Dielectric response. Perturbation theory, linear response, and finite electric fields".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_from_atoms_to_bulk.pdf From Atoms to Bulk systems]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_surface_science.pdf Surface Science]: A description of the examples "A bit of surface science".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_ammonia_flipping.pdf Ammonia Flipping]: A description of the examples "Transition State Search methods".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_h2o_on_tio2.pdf Adsorption of H2O on TiO2]: A description of the examples "Constrained Molecular Dynamics".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_dielectrics_and_RPA.pdf Dielectric properties and RPA]: A description of the examples "Dielectric properties and RPA".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Hybrid functionals ===<br />
<br />
[[bandgap of Si using different DFT+HF methods]]<br />
<br />
[[fcc Ni DOS with hybrid functional]]<br />
<br />
[[Si HSE bandstructure]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
=== Dielectric properties and RPA ===<br />
<br />
[[dielectric properties of SiC]]<br />
<br />
[[bandgap of Si in GW]]<br />
<br />
[[equilibrium volume of Si in the RPA]]<br />
<br />
[[bandstructure of SrVO3 in GW]]<br />
<br />
[[dielectric properties of Si using BSE]]<br />
<br />
[[model BSE calculation on Si]]<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2322ICAMM Rennes 20162016-08-26T15:37:42Z<p>Doris: /* Lectures */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics1.pdf DFT, PW, and PAW]: "VASP: The basics(1). DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics2.pdf electronic convergence, BZ sampling]: "VASP: The basics(2). electronic convergence, BZ sampling ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics3.pdf structure relaxation, MD]: "VASP: The basics(3). structure relaxation, phonons, MD...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Dielectric.pdf Dielectric properties]: "VASP: Dielectric response. Perturbation theory, linear response, and finite electric fields".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_from_atoms_to_bulk.pdf From Atoms to Bulk systems]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_surface_science.pdf Surface Science]: A description of the examples "A bit of surface science".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_ammonia_flipping.pdf Ammonia Flipping]: A description of the examples "Transition State Search methods".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_dielectrics_and_RPA.pdf Dielectric properties and RPA]: A description of the examples "Dielectric properties and RPA".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Hybrid functionals ===<br />
<br />
[[bandgap of Si using different DFT+HF methods]]<br />
<br />
[[fcc Ni DOS with hybrid functional]]<br />
<br />
[[Si HSE bandstructure]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
=== Dielectric properties and RPA ===<br />
<br />
[[dielectric properties of SiC]]<br />
<br />
[[bandgap of Si in GW]]<br />
<br />
[[equilibrium volume of Si in the RPA]]<br />
<br />
[[bandstructure of SrVO3 in GW]]<br />
<br />
[[dielectric properties of Si using BSE]]<br />
<br />
[[model BSE calculation on Si]]<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2225ICAMM Rennes 20162016-08-25T12:33:38Z<p>Doris: /* Tutorials */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics.pdf DFT, PW, and PAW]: "VASP: The basics. DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial1.pdf Tutorial1]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial2.pdf Tutorial2]: A description of the examples "A bit of surface science".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial_ammonia_flipping.pdf Tutorial_Ammonia_Flipping]: A description of the examples "Transition State Search methods".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Hybrid functionals ===<br />
<br />
[[bandgap of Si using different DFT+HF methods]]<br />
<br />
[[fcc Ni DOS with hybrid functional]]<br />
<br />
[[Si HSE bandstructure]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
=== Dielectric properties and RPA ===<br />
<br />
[[dielectric properties of SiC]]<br />
<br />
[[bandgap of Si in GW]]<br />
<br />
[[GW bandstructure of SrVO3 in GW]]<br />
<br />
[[dielectric properties of Si using BSE]]<br />
<br />
[[model BSE calculation on Si]]<br />
<br />
[[equilibrium volume of Si in the RPA]]<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Vibrational_Analysis_of_the_TS&diff=2199Vibrational Analysis of the TS2016-08-24T19:48:31Z<p>Doris: </p>
<hr />
<div>Description: the Improved Dimer Method needs an educated guess of the decay path, which is extimated from the hardest vibration mode with imaginary frequency of the TS geometry<br />
(which is a planar NH3 molecule):<br />
<br />
----<br />
*INCAR<br />
SYSTEM = Ammonia flipping<br />
IBRION = 5<br />
NSW = 1<br />
ALGO = F<br />
POTIM = 0.015<br />
EDIFF = 1e-8<br />
EDIFFG = -0.01<br />
NWRITE = 3<br />
<br />
*KPOINTS<br />
k-points<br />
0<br />
G<br />
1 1 1<br />
<br />
<br />
*POSCAR<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
H N<br />
3 1<br />
Direct<br />
0.6462 0.5736 0.5000<br />
0.5000 0.3547 0.5000<br />
0.3538 0.5736 0.5000<br />
0.5000 0.5000 0.5000<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/ammonia_flipping.tgz ammonia_flipping.tgz, sub-folder TS_vib]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Relaxed_geometry&diff=2198Relaxed geometry2016-08-24T19:47:32Z<p>Doris: Created page with "Description: calculate the relaxed geometry of NH3: the total energy is the energy of the initial state of the flipping reaction ---- *INCAR SYSTEM = Ammonia flipping IBRIO..."</p>
<hr />
<div>Description: calculate the relaxed geometry of NH3: the total energy is the energy of the initial state of the flipping reaction<br />
<br />
----<br />
*INCAR<br />
SYSTEM = Ammonia flipping<br />
IBRION = 2<br />
NSW = 10<br />
ALGO = N<br />
POTIM = 0.5<br />
EDIFF = 1e-6<br />
EDIFFG = -0.01<br />
NELMIN = 5<br />
<br />
<br />
*KPOINTS<br />
k-points<br />
0<br />
G<br />
1 1 1<br />
<br />
<br />
*POSCAR<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
H N<br />
3 1<br />
Selective dynamics<br />
Direct<br />
0.636429 0.567446 0.549205 T T T<br />
0.500000 0.364896 0.549205 T T T<br />
0.363571 0.567446 0.549205 T T T<br />
0.500000 0.500000 0.500000 F F F<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/ammonia_flipping.tgz ammonia_flipping.tgz, sub-folder scf]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2197ICAMM Rennes 20162016-08-24T19:43:10Z<p>Doris: /* Transition State Search of Ammonia */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics.pdf DFT, PW, and PAW]: "VASP: The basics. DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial1.pdf Tutorial1]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial2.pdf Tutorial2]: A description of the examples "A bit of surface science".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[relaxed geometry]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]]<br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=TS_search_using_the_Improved_Dimer_Method&diff=2196TS search using the Improved Dimer Method2016-08-24T19:42:39Z<p>Doris: Created page with "Description: ---- *INCAR SYSTEM = Ammonia flipping IBRION = 44 NSW = 100 EDIFF = 1e-6 EDIFFG = -0.01 *KPOINTS k-points 0 G 1 1 1 *POSCAR ammonia flipping..."</p>
<hr />
<div>Description:<br />
<br />
----<br />
*INCAR<br />
SYSTEM = Ammonia flipping<br />
IBRION = 44<br />
NSW = 100<br />
EDIFF = 1e-6<br />
EDIFFG = -0.01<br />
<br />
<br />
*KPOINTS<br />
k-points<br />
0<br />
G<br />
1 1 1<br />
<br />
<br />
*POSCAR<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
H N<br />
3 1<br />
Direct <br />
0.6462 0.5736 0.5000<br />
0.5000 0.3547 0.5000<br />
0.3538 0.5736 0.5000<br />
0.5000 0.5000 0.5000<br />
! decay direction<br />
0.000004 -0.000001 0.511990<br />
0.000000 -0.000003 0.547859<br />
-0.000004 -0.000001 0.511988<br />
0.000000 0.000000 -0.111986<br />
<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/ammonia_flipping.tgz ammonia_flipping.tgz, sub-folder improved_dimer]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Vibrational_Analysis_of_the_TS&diff=2195Vibrational Analysis of the TS2016-08-24T19:39:19Z<p>Doris: Created page with "Description: the Improved Dimer Method needs an educated guess of the decay path, which is extimated from the hardest vibration mode with imaginary frequency of the TS geometr..."</p>
<hr />
<div>Description: the Improved Dimer Method needs an educated guess of the decay path, which is extimated from the hardest vibration mode with imaginary frequency of the TS geometry<br />
(which is a plane NH3 molecule in this case :<br />
<br />
----<br />
*INCAR<br />
SYSTEM = Ammonia flipping<br />
IBRION = 5<br />
NSW = 1<br />
ALGO = F<br />
POTIM = 0.015<br />
EDIFF = 1e-8<br />
EDIFFG = -0.01<br />
NWRITE = 3<br />
<br />
*KPOINTS<br />
k-points<br />
0<br />
G<br />
1 1 1<br />
<br />
<br />
*POSCAR<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
H N<br />
3 1<br />
Direct<br />
0.6462 0.5736 0.5000<br />
0.5000 0.3547 0.5000<br />
0.3538 0.5736 0.5000<br />
0.5000 0.5000 0.5000<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/ammonia_flipping.tgz ammonia_flipping.tgz, sub-folder TS_vib]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=TS_search_using_the_NEB_Method&diff=2194TS search using the NEB Method2016-08-24T19:29:23Z<p>Doris: Created page with "Description: the Nudged Elastic Band Method generates an energy profile along a reaction path, using equidistant IMAGES along the path. The input geometries of the IMAGES are..."</p>
<hr />
<div>Description: the Nudged Elastic Band Method generates an energy profile along a reaction path,<br />
using equidistant IMAGES along the path. The input geometries of the IMAGES are interpolated between <br />
the geometries of the initial and the final states, e.g. using the script interpolatePOSCAR, which <br />
processes the con-catenated POSCAR files of the initial and the final state of the reaction (POSCAR_if).<br />
in the case of ammonia flipping the final state is a mirror of the initial state and need not be<br />
calculated explicitely.<br />
For each IMAGE, a separate sub-directory 00 ... (IMAGES+1) is needed, which contains all output of the <br />
respective IMAGE. The number of cores on which VASP is run has to be an integer multiple of the number of IMAGES. <br />
<br />
----<br />
*INCAR<br />
SYSTEM = Ammonia flipping<br />
IMAGES = 6<br />
SPRING = -5<br />
IBRION = 2<br />
NSW = 50<br />
ALGO = N<br />
POTIM = 1.0<br />
EDIFF = 1e-6<br />
<br />
<br />
*KPOINTS<br />
k-points<br />
0<br />
G<br />
1 1 1<br />
<br />
<br />
*POSCAR_if<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
3 1<br />
Direct<br />
0.636428 0.567457 0.5491645<br />
0.500000 0.364985 0.5491330<br />
0.363572 0.567457 0.5491645<br />
0.500000 0.500000 0.5000000<br />
ammonia flipping<br />
1.00000000000000<br />
6.000000 0.000000 0.000000<br />
0.000000 7.000000 0.000000<br />
0.000000 0.000000 8.000000<br />
3 1<br />
Direct<br />
0.636428 0.567457 0.4508355<br />
0.500000 0.364985 0.4508670<br />
0.363572 0.567457 0.4508355<br />
0.500000 0.500000 0.5000000<br />
<br />
<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/ammonia_flipping.tgz ammonia_flipping.tgz, sub-folder NEB]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ICAMM_Rennes_2016&diff=2191ICAMM Rennes 20162016-08-24T19:01:50Z<p>Doris: /* Exercises */</p>
<hr />
<div>== Lectures ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Basics.pdf DFT, PW, and PAW]: "VASP: The basics. DFT, plane waves, PAW, ...".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_Hybrids.pdf Hybrid functionals]: "VASP: Hybrid functionals".<br />
<br />
*[http://www.vasp.at/vasp-workshop/lectures/VASP_lecture_RPA.pdf RPA (GW and ACFDT)]: "VASP: Beyond DFT. The Random Phase Approximation".<br />
<br />
== Tutorials ==<br />
<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial1.pdf Tutorial1]: A description of the examples "Atoms and molecules" and "Simple bulk systems".<br />
*[http://www.vasp.at/vasp-workshop/tutorials/tutorial2.pdf Tutorial2]: A description of the examples "A bit of surface science".<br />
<br />
== Exercises ==<br />
:[[ICAMM_Rennes_2016_HOWTO|HOWTO: running the exercises]]<br />
<br />
=== Atoms and molecules ===<br />
<br />
[[O atom]]<br />
<br />
[[O atom spinpolarized]]<br />
<br />
[[O atom spinpolarized low symmetry]]<br />
<br />
[[O dimer]]<br />
<br />
[[CO]]<br />
<br />
[[CO vibration]]<br />
<br />
[[CO partial DOS]]<br />
<br />
[[H2O]]<br />
<br />
[[H2O vibration]]<br />
<br />
[[H2O molecular dynamics]]<br />
<br />
=== Simple bulk systems ===<br />
<br />
[[fcc Si]]<br />
<br />
[[fcc Si DOS]]<br />
<br />
[[fcc Si bandstructure]]<br />
<br />
[[cd Si]]<br />
<br />
[[cd Si volume relaxation]]<br />
<br />
[[cd Si relaxation]]<br />
<br />
[[fcc Ni]]<br />
<br />
[[graphite TS binding energy]]<br />
<br />
[[graphite MBD binding energy]]<br />
<br />
[[graphite interlayer distance]]<br />
<br />
<br />
=== A bit of surface science ===<br />
<br />
[[Ni 100 surface relaxation]]<br />
<br />
[[Ni 100 surface DOS]]<br />
<br />
[[Ni 100 surface bandstructure]]<br />
<br />
[[Ni 111 surface relaxation]]<br />
<br />
[[CO on Ni 111 surface]]<br />
<br />
[[Ni 111 surface high precision]]<br />
<br />
[[partial DOS of CO on Ni 111 surface]]<br />
<br />
[[vibrational frequencies of CO on Ni 111 surface]]<br />
<br />
[[STM of graphite]]<br />
<br />
[[STM of graphene]]<br />
<br />
=== Transition State Search of Ammonia ===<br />
<br />
[[Ground State]]<br />
<br />
[[TS search using the NEB Method]]<br />
<br />
[[Vibrational Analysis of the TS]]<br />
<br />
[[TS search using the Improved Dimer Method]] <br />
<br />
=== Magnetism on NiO ===<br />
<br />
[[NiO GGA]]<br />
<br />
[[NiO GGA+U]]<br />
<br />
[[NiO HSE06]]<br />
<br />
[[Estimation of J magnetic coupling]]<br />
<br />
[[Including the Spin-Orbit Coupling]]<br />
<br />
[[Determining the Magnetic Anisotropy]]<br />
<br />
[[Constraining the local magnetic moments]]<br />
<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP]][[Category:Workshops]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=LELF&diff=1630LELF2013-05-22T11:32:43Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|LELF|.TRUE. {{!}} .FALSE. |.FALSE.}}<br />
<br />
Description: {{TAG|LELF}} determines whether to create an<br />
{{FILE|ELFCAR}} file or not.<br />
----<br />
This file contains the so-called ELF (electron localization<br />
function) <ref name="silvi:nature:371"/><br />
<br />
If {{TAG|LELF}} is set, {{TAG|NPAR}}=1 has to be set explicitely in<br />
the {{FILE|INCAR}} file in addition<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|NPAR}}<br />
<br />
== References ==<br />
<references><br />
<ref name="silvi:nature:371">[http://www.nature.com/nature/journal/v371/n6499/pdf/371683a0.pdf B. Silvi and A. Savin, Nature 371, 683-686 (1994).]</ref><br />
</references><br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=LELF&diff=1629LELF2013-05-22T11:32:22Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|LELF|.TRUE. {{!}} .FALSE. |.FALSE.}}<br />
<br />
Description: {{TAG|LELF}} determines whether to create an<br />
{{FILE|ELFCAR}} file or not.<br />
----<br />
This file contains the so-called ELF (electron localization<br />
function) <ref name="silvi:nature:371"/><br />
<br />
If {{TAG|LELF}} is set, {{TAG|NPAR}}=1 has to be set explicitely in<br />
the {{FILE|INCAR}} file in addition<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|NPAR}}<br />
<br />
== References ==<br />
<references><br />
<ref name="silvi:nature:371">[http://www.nature.com/nature/journal/v371/n6499/pdf/371683a0.pdf B. Silvi and A. Savin, Nature 371, 683-686 (1994).]</ref><br />
</references><br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=LELF&diff=1628LELF2013-05-22T11:31:18Z<p>Doris: Created page with '{{TAGDEF|LELF|.TRUE. {{!}} .FALSE. |.FALSE.}} Description: {{TAG|LELF}} determines whether to create an {{FILE|ELFCAR}} file or not. ---- This file contains the so-called ELF (e…'</p>
<hr />
<div>{{TAGDEF|LELF|.TRUE. {{!}} .FALSE. |.FALSE.}}<br />
<br />
Description: {{TAG|LELF}} determines whether to create an<br />
{{FILE|ELFCAR}} file or not.<br />
----<br />
This file contains the so-called ELF (electron localization<br />
function) <ref name="silvi:nature:371"/><br />
<br />
If {{TAG|LELF}} is set, {{TAG|NPAR}}=1 has to be set explicitely in<br />
the {{FILE|INCAR}} file in addition<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|NPAR}}<br />
<br />
== References ==<br />
<references><br />
<ref name="silvi:nature:371">[http://www.nature.com/nature/journal/v371/n6499/pdf/371683a0.pdf B. Silvi and A. Savin, Nature 371, 683-686 (1994).]</ref><br />
</references><br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP|INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1627Category:INCAR2013-05-22T10:30:56Z<p>Doris: Blanked the page</p>
<hr />
<div></div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1626Category:INCAR2013-05-22T10:28:34Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|LELF|.TRUE. {{!}} .FALSE. |.FALSE.}}<br />
<br />
Description: {{TAG|LELF}} determines whether to create an<br />
{{FILE|ELFCAR}} file or not.<br />
----<br />
This file contains the so-called ELF (electron localization<br />
function) <ref name="silvi:nature:371"/><br />
<br />
If {{TAG|LELF}} is set, {{TAG|NPAR}}=1 has to be set explicitely in<br />
the {{FILE|INCAR}} file in addition<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|NPAR}}<br />
<br />
== References ==<br />
<references><br />
<ref name="silvi:nature:371">[http://www.nature.com/nature/journal/v371/n6499/pdf/371683a0.pdf<br />
B. Silvi and A. Savin, Nature 371, 683-686 (1994).]</ref><br />
</references><br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP|INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ENCUT&diff=1305ENCUT2012-08-31T15:11:44Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|ENCUT|[real]}}<br />
{{DEF|ENCUT| largest {{TAG|ENMAX}} from the {{FILE|POTCAR}}-file | }}<br />
<br />
Description: {{TAG|EMAX}} specifies the Cut-off energy for plane wave<br />
basis set in eV.<br />
<br />
----<br />
All plane-waves with a kinetic energy smaller than<br />
<math>E_{\mathrm{cut}}</math><br />
are included in the basis set: i.e.<br />
<br />
<math> | \mathbf{G} + \mathbf{k} | </math> with <math> E_{\mathrm{cut}} =<br />
\frac{\hbar^2}{2m} G^2_{\mathrm{cut}} </math><br />
<br />
The number of plane waves differs for each k-point, leading to a superior<br />
beahviour for e.g. energy-volume calculations. If the volume is increased the total number<br />
of plane waves changes fairly smoothly.<br />
The criterion <math>| \mathbf{G} | < G_{\mathrm{cut}} </math> (i.e. same basis set for each<br />
<math>\mathbf{k}</math>-point)<br />
would lead to a very rough energy-volume curve and, generally, slower energy convergence.<br />
<br />
Starting from version VASP 3.2 the {{FILE|POTCAR}} files contains a default<br />
{{TAG|ENMAX}} (and {{TAG|ENMIN}}) line,<br />
therefore it is in principle not necessary to specify {{TAG|ENCUT}} in<br />
the {{FILE|INCAR}} file. For calculations<br />
with more than one species, the maximum cutoff {{TAG|ENMAX}} or {{TAG|ENMIN}}<br />
value is used for the calculation (see {{TAG|PREC}}).<br />
For consistency reasons we still recommend to specify the cutoff manually<br />
in the {{FILE|INCAR}} file and keep in constant throughout a set of calculations.<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|ENMAX}},<br />
{{TAG|ENMIN}},<br />
{{TAG|PREC}},<br />
{{FILE|POTCAR}}<br />
[[Precision|Precision]]<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=ENCUT&diff=1304ENCUT2012-08-31T15:09:46Z<p>Doris: Created page with '{{TAGDEF|ENCUT|[real]}} {{DEF|ENCUT| largest {{TAG|ENMAX}} from the {{FILE|POTCAR}}-file | }} Description: {{TAG|EMAX}} specifies the Cut-off energy for plane wave basis set i…'</p>
<hr />
<div>{{TAGDEF|ENCUT|[real]}}<br />
{{DEF|ENCUT| largest {{TAG|ENMAX}} from the {{FILE|POTCAR}}-file | }}<br />
<br />
Description: {{TAG|EMAX}} specifies the Cut-off energy for plane wave<br />
basis set in eV.<br />
<br />
----<br />
All plane-waves with a kinetic energy smaller than<br />
<math>E_{\mathrm{cut}}</math><br />
are included in the basis set: i.e.<br />
<br />
<math> | \mathbf{G} + \mathbf{k} | </math> with <math> E_{\mathrm{cut}} =<br />
\frac{\hbar^2}{2m} G^2_{\mathrm{cut}} </math><br />
<br />
The number of plane waves differs for each k-point, leading to a superior<br />
beahviour for e.g. energy-volume calculations. If the volume is increased the total number<br />
of plane waves changes fairly smoothly.<br />
The criterion <math>| \mathbf{G} | < G_{\mathrm{cut}} </math> (i.e. same basis set for each<br />
<math>\mathbf{k}</math>-point)<br />
would lead to a very rough energy-volume curve and, generally, slower energy convergence.<br />
<br />
Starting from version VASP 3.2 the {{FILE|POTCAR}} files contains a default<br />
{{TAG|ENMAX}} (and {{TAG|ENMIN}}) line,<br />
therefore it is in principle not necessary to specify {{TAG|ENCUT}} in<br />
the {{FILE|INCAR}} file. For calculations<br />
with more than one species, the maximum cutoff {{TAG|ENMAX}} or {{TAG|ENMIN}}<br />
value is used for the calculation (see {{TAG|PREC}}).<br />
For consistency reasons we still recommend to specify the cutoff manually<br />
in the {{FILE|INCAR}} file and keep in constant throughout a set of calculations.<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|ENMAX}},<br />
{{TAG|ENMIN}},<br />
{{FILE|POTCAR}}<br />
[[Precision|Precision]]<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=EMAX&diff=1303EMAX2012-08-31T13:24:02Z<p>Doris: Created page with '{{TAGDEF|EMAX|[real]}} {{DEF|EMAX| highest KS-eigenvalue + <math>\Delta</math> | }} Description: {{TAG|EMAX}} specifies the upper boundary of the energy range for the evaluati…'</p>
<hr />
<div>{{TAGDEF|EMAX|[real]}}<br />
{{DEF|EMAX| highest KS-eigenvalue + <math>\Delta</math> | }}<br />
<br />
Description: {{TAG|EMAX}} specifies the upper boundary of the energy range<br />
for the evaluation of the DOS<br />
----<br />
The DOS is evaluated each {{TAG|NBLOCK}} steps, {{FILE|DOSCAR}} is updated each {{TAG|NBLOCK}}*{{TAG|KBLOCK}} steps.<br />
<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMIN}}, {{TAG|NEDOS}},<br />
{{FILE|DOSCAR}}<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=EMIN&diff=1302EMIN2012-08-31T13:21:58Z<p>Doris: Created page with '{{TAGDEF|EMIN|[real]}} {{DEF|EMIN| lowest KS-eigenvalue - <math>\Delta</math> | }} Description: {{TAG|EMAX}} specifies the lower boundary of the energy range for the evaluati…'</p>
<hr />
<div>{{TAGDEF|EMIN|[real]}}<br />
{{DEF|EMIN| lowest KS-eigenvalue - <math>\Delta</math> | }}<br />
<br />
Description: {{TAG|EMAX}} specifies the lower boundary of the energy range <br />
for the evaluation of the DOS<br />
----<br />
The DOS is evaluated each {{TAG|NBLOCK}} steps, {{FILE|DOSCAR}} is updated<br />
each {{TAG|NBLOCK}}*{{TAG|KBLOCK}} steps. <br />
<br />
<br />
'''Mind''': If you are not sure where the region of interest lies, set<br />
{{TAG|EMIN}} to a value larger than {{TAG|EMAX}}<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMIN}}, {{TAG|NEDOS}},<br />
{{FILE|DOSCAR}}<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1301Category:INCAR2012-08-31T13:18:01Z<p>Doris: Blanked the page</p>
<hr />
<div></div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1300Category:INCAR2012-08-31T13:17:15Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|EMIN|[real]}}<br />
{{DEF|EMIN| lowest KS-eigenvalue - <math>Delta</math><br />
Description: {{TAG|MIN}} specifies the lower boundary of the energy range<br />
for the evaluation of the DOS<br />
----<br />
The DOS is evaluated each {{TAG|NBLOCK}} steps, {{FILE|DOSCAR}} is updated each {{TAG|NBLOCK}}*{{TAG|KBLOCK}} steps.<br />
<br />
'''Mind''': If you are not sure where the region of interest lies, set<br />
{{TAG|EMIN}} to a value larger than {{TAG|EMAX}}<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMAX}}, {{TAG|NEDOS}},<br />
{{FILE|DOSCAR}}<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1299Category:INCAR2012-08-31T13:09:47Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|EMAX|[real]}}<br />
{{DEF|EMAX| lowest KS-eigenvalue + <math>\Delta</math> |}}<br />
<br />
Description: {{TAG|EMAX}} specifies the lower boundary of the energy range<br />
for the evaluation of the DOS<br />
----<br />
The DOS is evaluated each {{TAG|NBLOCK}} steps, {{FILE|DOSCAR}} is updated each {{TAG|NBLOCK}}*{{TAG|KBLOCK}} steps.<br />
<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMIN}}, {{TAG|NEDOS}},<br />
{{FILE|DOSCAR}}<br />
<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP|INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Category:INCAR&diff=1298Category:INCAR2012-08-31T13:08:03Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|EMIN|[real]}}<br />
{{DEF|EMIN| lowest KS-eigenvalue - <math>\Delta</math> |}}<br />
<br />
Description: {{TAG|EMIN}} specifies the lower boundary of the energy range<br />
for the evaluation of the DOS<br />
----<br />
The DOS is evaluated each {{TAG|NBLOCK}} steps, {{FILE|DOSCAR}} is updated each {{TAG|NBLOCK}}*{{TAG|KBLOCK}} steps.<br />
<br />
'''Mind''': If you are not sure where the region of interest lies, set<br />
{{TAG|EMIN}} to a value larger than {{TAG|EMAX}}<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMAX}}, {{TAG|NEDOS}},<br />
{{FILE|DOSCAR}}<br />
<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:VASP|INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=NEDOS&diff=1297NEDOS2012-08-31T12:50:33Z<p>Doris: Created page with '{{TAGDEF|NEDOS|[integer]|<math>301</math>}} Description: {{TAG|NEDOS}} specifies number of gridpoints on which the DOS is evaluated ---- The energy range between {{TAG|EMIN}} an…'</p>
<hr />
<div>{{TAGDEF|NEDOS|[integer]|<math>301</math>}}<br />
<br />
Description: {{TAG|NEDOS}} specifies number of gridpoints on which the DOS is evaluated<br />
----<br />
The energy range between {{TAG|EMIN}} and {{TAG|EMAX}} is divided into<br />
{{TAG|NEDOS}} intervals, the DOS for each corresponding energy is written in<br />
{{FILE|DOSCAR}}.<br />
<br />
'''Mind''': If the DOS has narrow peaks, the default {{TAG|NEDOS}} may be too<br />
small to resolve all peaks properly. It may be helpful to compare the DOS<br />
to the integrated DOS (also written on {{FILE|DOSCAR}}) to find out whether<br />
this is the case: at least one peak should show up at every step of the integrated DOS.<br />
If so, the smallest peak widths from the dispersion of<br />
the respective bands can be estimated by having a look at the Kohn-Sham eigenvalues written<br />
in {{FILE|OUTCAR}}. {{TAG|NEDOS}} has to be chosen sufficiently large to resolve this dispersion. Alternatively, the<br />
energy interval defined by {{TAG|EMIN}} and {{TAG|EMAX}} can be modified.<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|EMIN}}, {{TAG|EMAX}},<br />
{{FILE|DOSCAR}}<br />
<br />
----<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=CO_vibration&diff=1291CO vibration2012-06-09T23:12:15Z<p>Doris: </p>
<hr />
<div>*INCAR<br />
SYSTEM = CO molecule in a box<br />
ISMEAR = 0 ! Gaussian smearing<br />
IBRION = 5 ! use the conjugate gradient algorithm<br />
NFREE = 2 ! central differences<br />
POTIM = 0.02 ! 0.02 A stepwidth <br />
NSW = 1 ! ionic steps > 0<br />
<br />
*KPOINTS<br />
Gamma-point only<br />
1 ! one k-point<br />
rec ! in units of the reciprocal lattice vector<br />
0 0 0 1 ! 3 coordinates and weight<br />
<br />
*POSCAR<br />
CO molecule in a box<br />
1.0 ! universal scaling parameters<br />
8.0 0.0 0.0 ! lattice vector a(1)<br />
0.0 8.0 0.0 ! lattice vector a(2)<br />
0.0 0.0 8.0 ! lattice vector a(3)<br />
1 1 ! number of atoms for each species<br />
sel ! selective degrees of freedom are changed<br />
cart ! positions in cartesian coordinates<br />
0 0 0 F F T ! first atom<br />
0 0 1.143 F F T ! second atom<br />
<br />
alternatively, try to fix one of the atoms completely.<br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/1_6_COvib.tgz 1_6_COvib.tgz]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1276Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-09T15:55:27Z<p>Doris: </p>
<hr />
<div><b>Description</b>: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom Pt@Pt(001) is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward <br />
<br />
inputs for a fast, preliminary estimate are given here and in Pt_NEB_fast.tgz (<b>mind</b> this "quick and dirty" setup is only suitable to learn about principles of the setup of a NEB calculation; the results of the NEB run with this minimal set of parameters do <b>not</b> reproduce the experimentally found behaviour), for a more time-consuming, but more accurate setup (larger number of Pt layers, denser k-mesh, higher {{TAG|PREC}} and {{TAG|ENCUT}}) please use the files untarred from Pt_NEB.tgz: <br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
POTIM = 0.5<br />
NSW = 20<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (clean surface)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024<br />
1.0 0.0 0.0<br />
0.0 1.0 0.0<br />
0.0 0.0 3.0<br />
Pt<br />
12<br />
Selective<br />
Direct<br />
0.25 0.25 0.11785 F F F<br />
0.75 0.25 0.11785 F F F<br />
0.25 0.75 0.11785 F F F<br />
0.75 0.75 0.11785 F F F<br />
0.00 0.00 0.23570 F F T<br />
0.00 0.50 0.23570 F F T<br />
0.50 0.00 0.23570 F F T<br />
0.50 0.50 0.23570 F F T<br />
0.25 0.25 0.35355 F F T<br />
0.75 0.25 0.35355 F F T<br />
0.25 0.75 0.35355 F F T<br />
0.75 0.75 0.35355 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), hollow)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt <br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0000000000000000 0.0000000000000000 0.2341409911878811 T T T<br />
0.0000000000000000 0.5000000000000000 0.2344158754007225 T T T<br />
0.5000000000000000 0.0000000000000000 0.2377721273226986 T T T<br />
0.5000000000000000 0.5000000000000000 0.2341409911878811 T T T<br />
0.2500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.2500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.0000000000000000 0.5000000000000000 0.4492270704381683 T T T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), bridge)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0002686432543183 0.0000000000000000 0.2356407813553420 T T T<br />
0.0014220524373488 0.5000000000000000 0.2356795143373628 T T T<br />
0.4997313567456815 0.0000000000000000 0.2356407813553420 T T T<br />
0.4985779475626512 0.5000000000000000 0.2356795143373628 T T T<br />
0.2500000000000000 0.2341977119064422 0.3525947402192897 F T T<br />
0.7500000000000000 0.2518717446753760 0.3518647397661007 T T T<br />
0.2500000000000000 0.7658022880935580 0.3525947402192897 F T T<br />
0.7500000000000000 0.7481282553246233 0.3518647397661007 T T T<br />
0.2500000000000000 0.5000000000000000 0.4716518885541170 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), top<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
-0.0014262288827347 -0.0014262288827347 0.2348121710889565 T T T<br />
-0.0014262288827347 0.5014262288827348 0.2348121710889565 T T T<br />
0.5014262288827348 -0.0014262288827347 0.2348121710889565 T T T<br />
0.5014262288827348 0.5014262288827348 0.2348121710889565 T T T<br />
0.2500000000000000 0.2500000000000000 0.3433443664932221 F F T<br />
0.7500000000000000 0.2500000000000000 0.3546231232810972 T T T<br />
0.2500000000000000 0.7500000000000000 0.3546231232810972 T T T<br />
0.7500000000000000 0.7500000000000000 0.3516055254412989 T T T<br />
0.2500000000000000 0.2500000000000000 0.4861522106341429 F F T<br />
</pre><br />
<br />
the NEB calculation should be done a follows:<br />
<br />
1. run the job from a parent directory containing the files {{FILE|INCAR}}, {{FILE|POTCAR}},{{FILE|KPOINTS}} and the run-script of the job <br />
<br />
2. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in {{FILE|INCAR}}, this corresponds to the parameter {{TAG|IMAGES}}<br />
<br />
3. generate sub-directories 00 (containing the {{FILE|POSCAR}} of the initial geometry i), ... 0(N+1) (containing the {{FILE|POSCAR}} of the final geometry f of the jump). The {{FILE|POSCAR}} files of the intermediate steps, to be interpolated between {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>f</sub><br />
are stored in the directories 01 .. 0N. Calculations are <b>only</b> done for these intermediate steps, the optimization of the geometries is done under the constraint that the relaxing atoms remain on a plane perpendicular to the hypertangent of the diffusion path. All all output files {{FILE|OUTCAR}}, {{FILE|CONTCAR}}, {{FILE|OSZICAR}} .. of the NEB-steps run are written to these subdirectories.<br />
<br />
in the present excercise, the required precision,... is reduced to a minimum (the files are found in [http://www.vasp.at/vasp-workshop/example/Pt_NEB_fast.tgz Pt_NEB_fast.tgz]) to save computing time, a<br />
more reliable setup is saved in [http://www.vasp.at/vasp-workshop/examples/Pt_NEB.tgz Pt_NEB.tgz])<br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
NSW = 10<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
IMAGES = 2 # 2 intermediate geometries for the NEB<br />
SPRING = -5 # spring constant<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (of the initial state, in directory 00)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000 <br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.256381 0.243619 0.347171<br />
0.743619 0.243619 0.347171<br />
0.256381 0.756381 0.347171<br />
0.743619 0.756381 0.347171<br />
0.000000 0.500000 0.444316<br />
</pre><br />
<br />
*POSCAR (of the final state, in directory 03)<br />
<br />
<pre><br />
<br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.500000 0.000000 0.444316<br />
0.756381 0.256381 0.347171<br />
0.243619 0.743619 0.347171<br />
0.756381 0.743619 0.347171<br />
0.243619 0.256381 0.347171<br />
</pre><br />
<br />
4. concatenate the {{FILE|POSCAR}} files of i and f to the file {{FILE|POSCAR1_POSCAR2}}<br />
MIND: <br />
<br />
-- these files must not include the lines with the names of the atoms (vasp.5.2 only) and 'Selective Dynamics',<br />
<br />
-- there must be no blank line between the POSCARS<br />
<br />
-- the block with the velocities of the atoms must be deleted<br />
<br />
-- be careful to check that in {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>j</sub> all atoms are on the same side of the supercell to avoid that an atom that actually jumps across the origin of the cell is dragged through the cell by the interpolation of the positions.<br />
<br />
5. interpolate the starting geometries of the {{TAG|IMAGES}}, this can be done by using the following script <br />
<br />
interpolatePOSCAR {{FILE|POSCAR1_POSCAR2}}, the interpolated files are written into the respective subdirectories <br />
00 ... 0(N+1)<br />
<br />
<br />
* interpolatePOSCAR<br />
<br />
<pre><br />
file=$1<br />
if [ ! -x $file ]<br />
then<br />
usage: interpolatePOS POSCAR1_POSCAR2<br />
fi<br />
<br />
awk <$file '<br />
BEGIN { rep=4; center=0 }<br />
/center/ { center=1}<br />
/rep/ { rep=$2 }<br />
{ line=line+1<br />
if ( second != 1 ) {<br />
if ( line == 6 ) {<br />
lines = $1 + $2 + $3 + 7<br />
print "found ",lines," ions"<br />
head[line] = $0<br />
} else if ( line < 8 )<br />
head[line] = $0<br />
else<br />
{<br />
x[line-7] = $1 ; y[line-7] = $2 ; z[line-7] = $3<br />
if (line==lines) {<br />
line=0; second=1;<br />
print "first set read"<br />
}<br />
}<br />
} else {<br />
if ( line >= 8 )<br />
{<br />
x2[line-7] = $1; y2[line-7] = $2 ; z2[line-7] = $3 }<br />
if (line==lines) {<br />
print "second set read"<br />
}<br />
}<br />
}<br />
END {<br />
lines=lines-7<br />
for ( line=1; line<=lines ; line ++ ) {<br />
cx1=cx1+ x[line] ; cy1=cy1+ y[line] ; cz1=cz1+ z[line]<br />
cx2=cx2+ x2[line]; cy2=cy2+ y2[line]; cz2=cz2+ z2[line]<br />
}<br />
if (center) {<br />
cx=(cx2-cx1)/lines<br />
cy=(cy2-cy1)/lines<br />
cz=(cz2-cz1)/lines<br />
print "center of mass for second cell will be shifted by",cx,cy,cz<br />
}<br />
<br />
for ( i=0; i<rep ; i++ ) {<br />
file="0" i "/POSCAR"<br />
print "writing to " file<br />
for (line=1; line<=7 ; line++ )<br />
print head[line] >file<br />
for ( line=1; line<=lines ; line ++ ) {<br />
b=i/(rep-1)<br />
a=(rep-1-i)/(rep-1)<br />
dx=a*x[line] + b*(x2[line]-cx)<br />
dy=a*y[line] + b*(y2[line]-cy)<br />
dz=a*z[line] + b*(z2[line]-cz)<br />
<br />
printf " %10.6f %10.6f %10.6f\n",dx,dy,dz >file<br />
}<br />
}<br />
}'<br />
</pre><br />
<br />
NOTE: the total number of steps is explicitely given in line 8 of the script (rep=, rep = {{TAG|IMAGES}}+2). If a dfferent number of {{TAG|IMAGES}} is chosen, this parameter has to be changed. <br />
<br />
<b>alternatively</b> the name of the input file and the number of images can be passed as options to interpolatePOSCAR: interpolatePOSCAR <fn> <{{TAG|IMAGES}}+2><br />
<br />
6. run vasp: <br />
<br />
<b>MIND</b>: the number of CPUs to be used has to be an integer multiple of {{TAG|IMAGES}}<br />
<br />
7. if convergence is not reached within {{TAG|NSW}} steps, the calculation can be continued by a continuation run, just like for a standard ionic relaxation.<br />
<br />
8. HINT: better convergence is usually achieved if the number of {{TAG|IMAGES}} is rather low (up to 4). If the region close to the transition state is to be<br />
refined, one can do another NEB-calculation, using the ionic configurations of the IMAGES adjacent to the transition state as the new initial and final<br />
states for the follow-up run. <br />
<br />
9: obtain the barrier along diffusion path 00-03 by interpolation (spline)<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Downloads ==<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB.tgz Pt_NEB.tgz],<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB_fast.tgz Pt_NEB_fast.tgz]<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=H2O_molecular_dynamics&diff=1266H2O molecular dynamics2012-06-09T14:35:29Z<p>Doris: </p>
<hr />
<div>*INCAR<br />
PREC = Normal ! standard precision <br />
ENMAX = 400 ! cutoff should be set manually<br />
ISMEAR = 0 ; SIGMA = 0.1<br />
ISYM = 0 ! strongly recommended for MD<br />
IBRION = 0 ! molecular dynamics<br />
NSW = 100 ! 100 steps<br />
POTIM = 1.0 ! timestep 1 fs<br />
SMASS = -3 ! Nose Hoover thermostat<br />
TEBEG = 2000 ; TEEND = 2000 ! temperature<br />
<br />
*KPOINTS<br />
Gamma-point only<br />
1 ! one k-point<br />
rec ! in units of the reciprocal lattice vector<br />
0 0 0 1 ! 3 coordinates and weight<br />
<br />
*POSCAR<br />
H2O _2<br />
0.52918 ! scaling parameter<br />
12 0 0<br />
0 12 0<br />
0 0 12<br />
1 2<br />
select<br />
cart<br />
0.00 0.00 0.00 T T F<br />
1.10 -1.43 0.00 T T F<br />
1.10 1.43 0.00 T T F<br />
<br />
the pair correlation function can be visualized using e.g. the following script:<br />
<br />
*plot_PCDAT<br />
<pre><br />
awk <PCDAT >PCDAT.xy '<br />
NR==8 { pcskal=$1}<br />
NR==9 { pcfein=$1}<br />
NR>=13 {<br />
line=line+1<br />
if (line==257) {<br />
print " "<br />
line=0<br />
}<br />
else<br />
print (line-0.5)*pcfein/pcskal,$1<br />
}<br />
'<br />
cat >plotfile<<!<br />
# set term postscript enhanced colour lw 2 "Helvetica" 20<br />
# set output "pair_correlation.eps"<br />
set title "pair-correlation of H2O at 2000 K"<br />
set xlabel "r [Angstrom]"<br />
set ylabel "g(r)"<br />
plot [0:15] "PCDAT.xy" w lines<br />
!<br />
gnuplot -persist plotfile<br />
</pre><br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/1_10_H2Omd.tgz 1_10_H2Omd.tgz]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Liquid_Si_-_Freezing&diff=1257Liquid Si - Freezing2012-06-08T17:13:42Z<p>Doris: </p>
<hr />
<div>Description: <tt>script</tt> performs molecular dynamics runs on liquid Si a decreasing temperatures, starting at 2000 K and ending at 800 K. This should contain the transition from liquid Si to crystalline Si (amorphous).<br />
<br />
----<br />
*script<br />
<pre><br />
for i in 2000 1900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800<br />
do<br />
cat >INCAR <<!<br />
SYSTEM = Si<br />
# electronic degrees <br />
LREAL = A # real space projection<br />
PREC = Normal # chose Low only after tests<br />
EDIFF = 1E-5 # do not use default (too large drift)<br />
ISMEAR = -1 ; SIGMA = 0.130 # Fermi smearing: 1500 K 0.086 10-3<br />
ALGO = Very Fast # recommended for MD (fall back ALGO = Fast)<br />
MAXMIX = 40 # reuse mixer from one MD step to next<br />
ISYM = 0 # no symmetry <br />
NELMIN = 4 # minimum 4 steps per time step, avoid breaking after 2 steps<br />
<br />
# MD (do little writing to save disc space)<br />
IBRION = 0 ; NSW = 400 ; NWRITE = 0 ; LCHARG = .FALSE. ; LWAVE = .FALSE.<br />
TEBEG = $i ; TEEND = $i<br />
# canonic (Nose) MD with XDATCAR updated every 10 steps<br />
SMASS = 3 ; NBLOCK = 10 ; POTIM = 3<br />
!<br />
mpirun -np 2 /path/to/your/vasp/executable<br />
cp XDATCAR XDATCAR.$i<br />
cp OUTCAR OUTCAR.$i<br />
cp PCDAT PCDAT.$i<br />
cp CONTCAR CONTCAR.$i<br />
cp POSCAR POSCAR.$i<br />
cp OSZICAR OSZICAR.$i<br />
cp CONTCAR POSCAR<br />
done<br />
</pre><br />
<br />
'''Mind''': You will have to set the correct path to your VASP executable and invoke VASP with the correct command (e.g., in the above: <tt>mpirun -np 2</tt>).<br />
<br />
*KPOINTS<br />
<pre><br />
test<br />
0 0 0<br />
monk<br />
1 1 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR<br />
Si<br />
15.12409564534287297131<br />
0.5000000000000000 0.5000000000000000 0.0000000000000000<br />
0.0000000000000000 0.5000000000000000 0.5000000000000000<br />
0.5000000000000000 0.0000000000000000 0.5000000000000000<br />
48<br />
Direct<br />
0.8550657259653851 0.3204575801875221 0.6180363868822553<br />
0.6045454476433229 0.0546379652195404 0.1629680405553871<br />
0.4803889256776521 0.2999635319377835 0.0131251454718051<br />
0.8413504226620471 0.7598095803296524 0.1917781560970181<br />
0.9754163118144437 0.6134171268457649 0.7421364242876367<br />
0.2668229391055025 0.0066502741664650 0.0031140604380929<br />
0.8935777664000575 0.3324172908647429 0.9535738516718881<br />
0.0527608886321274 0.5249316429131962 0.5293744880144071<br />
0.4396089233132741 0.7564833235979471 0.5665855438788387<br />
0.5907859878830199 0.5198033580597228 0.3581725847640679<br />
0.2120832721474721 0.4042899613004446 0.7921535013319151<br />
0.0225803885096466 0.8414911198321031 0.1209255489569852<br />
0.0992500701525566 0.3917384466892963 0.3612433325214984<br />
0.9673794138223195 0.5206425706394114 0.1719623236201897<br />
0.2774602656926126 0.8480860088162007 0.2673309412777037<br />
0.0196991774214161 0.8282178425383616 0.6986213756952502<br />
0.3570927152895376 0.2951488295546784 0.2651851032568589<br />
0.1663829731894614 0.9766237917413699 0.6051764245375237<br />
0.4931841331696695 0.8689890620771937 0.2612357008392290<br />
0.8006473407426477 0.1033419073227807 0.4706563716777467<br />
0.0161340851939779 0.9953827418297991 0.8853439845676159<br />
0.7827740166661069 0.1821830067208054 0.9399555168314748<br />
0.0720651739141343 0.2539424963694544 0.6857919074323433<br />
0.4443385370769313 0.0486404637002326 0.4180706114402839<br />
0.7055263679666055 0.6802623819082319 0.7983614866719116<br />
0.2237125282521105 0.4055474352416297 0.0077044950891134<br />
0.2963682069847125 0.5771265542042112 0.2019757061665083<br />
0.2782449529809642 0.0451513130915826 0.7644934848784113<br />
0.9312079203181675 0.9090938018377080 0.3429249881187518<br />
0.6341882597200124 0.2969253226419481 0.3227590981305088<br />
0.3587691103780569 0.1061057273904179 0.0931868777500710<br />
0.8710437838676732 0.6541301230631744 0.4261617089364881<br />
0.6784300588817769 0.3263889355408940 0.5560491395978739<br />
0.5597052314845080 0.0174390112509929 0.6129003207931863<br />
0.0595962318875451 0.1019295953521402 0.3340999072062676<br />
0.7689671766774326 0.1768870209149794 0.1604177484299765<br />
0.9603661624482890 0.3311649224573259 0.1439224909303592<br />
0.3792868784787023 0.2806150985211180 0.4921541531665999<br />
0.8079860889823454 0.9194188799048340 0.9131036494263627<br />
0.3002081239026374 0.7834053620019006 0.8650323716139056<br />
0.4704528574512951 0.7221628305989689 0.9746107190983403<br />
0.2886552568292480 0.5927625600330780 0.4239421203107919<br />
0.4116743942942291 0.2198943758058664 0.7072597030225044<br />
0.2104494234814825 0.6457654201409418 0.8275863924787099<br />
0.6784628197745537 0.7205455185203838 0.1093053357228383<br />
0.6344130299021448 0.1650970001101275 0.8037018707797643<br />
0.3965793440603315 0.5364088146415013 0.6064549771969059<br />
0.6686412136025504 0.7848666926903073 0.5681234351534038<br />
<br />
to analyse the diffusion behaviour at a certain temperature T, the data read from {{FILE|XDATCAR.[T]}} can be processed<br />
using the following script:<br />
<br />
*diffusion<br />
<br />
<pre><br />
awk <XDATCAR >diffusion.xy '<br />
#<br />
# simple module function<br />
#<br />
function mod(x,y) { return x-int(x/y)*y }<br />
function minim(x) { return mod(x+2.5,1.0)-0.5 }<br />
#<br />
# calculate mean square displacement<br />
#<br />
function diff() {<br />
d=0<br />
for (ion=1; ion<=ions; ion++) {<br />
dx=minim(xn[ion]-x[ion])<br />
dy=minim(yn[ion]-y[ion])<br />
dz=minim(zn[ion]-z[ion])<br />
<br />
xn[ion]=x[ion]+dx<br />
yn[ion]=y[ion]+dy<br />
zn[ion]=z[ion]+dz<br />
<br />
<br />
d=d+(xn[ion]-x0[ion])*(xn[ion]-x0[ion])*a1*a1<br />
d=d+(yn[ion]-y0[ion])*(yn[ion]-y0[ion])*a2*a2<br />
d=d+(zn[ion]-z0[ion])*(zn[ion]-z0[ion])*a3*a3<br />
}<br />
# d=d/(set*t)/6<br />
d=d/6<br />
print set*t,d<br />
}<br />
#<br />
# set the number of ions<br />
#<br />
NR==1 { ions = $1 }<br />
NR==2 { a1=$2*10^10 ; a2=$3*10^10 ; a3=$4*10^10 ; t=$5*10^12 }<br />
# <br />
# at this point a complete set of ionic positions has been found<br />
#<br />
mod(NR-6,ions+1)==0 {<br />
if (set>=2) diff()<br />
if (set==1) {<br />
for (ion=1; ion<=ions; ion++) {<br />
x0[ion]=xn[ion]<br />
y0[ion]=yn[ion]<br />
z0[ion]=zn[ion]<br />
}<br />
}<br />
for (ion=1; ion<=ions; ion++) {<br />
x[ion]=xn[ion]<br />
y[ion]=yn[ion]<br />
z[ion]=zn[ion]<br />
}<br />
head=headn<br />
headn=$0<br />
set=set+1<br />
}<br />
# store coordinates<br />
mod(NR-6,ions+1)>0 {<br />
ion=mod(NR-6,ions+1)<br />
xn[ion]=$1<br />
yn[ion]=$2<br />
zn[ion]=$3<br />
}<br />
'<br />
</pre><br />
<br />
The pair-correlation function written on {{FILE|PCDAT.[T]}} should be processed using the script<br />
<br />
*PCDATtoPCDATxy<br />
<br />
<pre><br />
awk <PCDAT >PCDAT.xy '<br />
NR==8 { pcskal=$1}<br />
NR==9 { pcfein=$1}<br />
NR>=13 {<br />
line=line+1<br />
if (line==257) {<br />
print " "<br />
line=0<br />
}<br />
else<br />
print (line-0.5)*pcfein/pcskal,$1<br />
}<br />
'<br />
</pre><br />
== Download ==<br />
[http://www.vasp.at/vasp-workshop/examples/Si_liquid.tgz Si_liquid.tgz]<br />
<br />
----<br />
[[VASP_example_calculations|To the list of examples]] or to the [[The_VASP_Manual|main page]]<br />
<br />
[[Category:Examples]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1255Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T15:49:21Z<p>Doris: </p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom Pt@Pt(001) is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward (inputs for a fast, preliminary estimate are given here and in Pt_NEB_fast.tgz, for a more time-consuming, but more accurate setup (larger number of Pt layers, denser k-mesh, higher {{TAG|PREC}} and {{TAG|ENCUT}}) please use the files untarred from Pt_NEB.tgz: <br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
POTIM = 0.5<br />
NSW = 20<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (clean surface)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024<br />
1.0 0.0 0.0<br />
0.0 1.0 0.0<br />
0.0 0.0 3.0<br />
Pt<br />
12<br />
Selective<br />
Direct<br />
0.25 0.25 0.11785 F F F<br />
0.75 0.25 0.11785 F F F<br />
0.25 0.75 0.11785 F F F<br />
0.75 0.75 0.11785 F F F<br />
0.00 0.00 0.23570 F F T<br />
0.00 0.50 0.23570 F F T<br />
0.50 0.00 0.23570 F F T<br />
0.50 0.50 0.23570 F F T<br />
0.25 0.25 0.35355 F F T<br />
0.75 0.25 0.35355 F F T<br />
0.25 0.75 0.35355 F F T<br />
0.75 0.75 0.35355 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), hollow)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt <br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0000000000000000 0.0000000000000000 0.2341409911878811 T T T<br />
0.0000000000000000 0.5000000000000000 0.2344158754007225 T T T<br />
0.5000000000000000 0.0000000000000000 0.2377721273226986 T T T<br />
0.5000000000000000 0.5000000000000000 0.2341409911878811 T T T<br />
0.2500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.2500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.0000000000000000 0.5000000000000000 0.4492270704381683 T T T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), bridge)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0002686432543183 0.0000000000000000 0.2356407813553420 T T T<br />
0.0014220524373488 0.5000000000000000 0.2356795143373628 T T T<br />
0.4997313567456815 0.0000000000000000 0.2356407813553420 T T T<br />
0.4985779475626512 0.5000000000000000 0.2356795143373628 T T T<br />
0.2500000000000000 0.2341977119064422 0.3525947402192897 F T T<br />
0.7500000000000000 0.2518717446753760 0.3518647397661007 T T T<br />
0.2500000000000000 0.7658022880935580 0.3525947402192897 F T T<br />
0.7500000000000000 0.7481282553246233 0.3518647397661007 T T T<br />
0.2500000000000000 0.5000000000000000 0.4716518885541170 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), top<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
-0.0014262288827347 -0.0014262288827347 0.2348121710889565 T T T<br />
-0.0014262288827347 0.5014262288827348 0.2348121710889565 T T T<br />
0.5014262288827348 -0.0014262288827347 0.2348121710889565 T T T<br />
0.5014262288827348 0.5014262288827348 0.2348121710889565 T T T<br />
0.2500000000000000 0.2500000000000000 0.3433443664932221 F F T<br />
0.7500000000000000 0.2500000000000000 0.3546231232810972 T T T<br />
0.2500000000000000 0.7500000000000000 0.3546231232810972 T T T<br />
0.7500000000000000 0.7500000000000000 0.3516055254412989 T T T<br />
0.2500000000000000 0.2500000000000000 0.4861522106341429 F F T<br />
</pre><br />
<br />
the NEB calculation should be done a follows:<br />
<br />
1. run the job from a parent directory containing the files {{FILE|INCAR}}, {{FILE|POTCAR}},{{FILE|KPOINTS}} and the run-script of the job <br />
<br />
2. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in {{FILE|INCAR}}, this corresponds to the parameter {{TAG|IMAGES}}<br />
<br />
3. generate sub-directories 00 (containing the {{FILE|POSCAR}} of the initial geometry i), ... 0(N+1) (containing the {{FILE|POSCAR}} of the final geometry f of the jump). The {{FILE|POSCAR}} files of the intermediate steps, to be interpolated between {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>f</sub><br />
are stored in the directories 01 .. 0N. Calculations are <b>only</b> done for these intermediate steps, the optimization of the geometries is done under the constraint that the relaxing atoms remain on a plane perpendicular to the hypertangent of the diffusion path. All all output files {{FILE|OUTCAR}}, {{FILE|CONTCAR}}, {{FILE|OSZICAR}} .. of the NEB-steps run are written to these subdirectories.<br />
<br />
in the present excercise, the required precision,... is reduced to a minimum (the files are found in [http://www.vasp.at/vasp-workshop/example/Pt_NEB_fast.tgz Pt_NEB_fast.tgz]) to save computing time, a<br />
more reliable setup is saved in [http://www.vasp.at/vasp-workshop/examples/Pt_NEB.tgz Pt_NEB.tgz])<br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
NSW = 10<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
IMAGES = 2 # 2 intermediate geometries for the NEB<br />
SPRING = -5 # spring constant<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (of the initial state, in directory 00)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000 <br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.256381 0.243619 0.347171<br />
0.743619 0.243619 0.347171<br />
0.256381 0.756381 0.347171<br />
0.743619 0.756381 0.347171<br />
0.000000 0.500000 0.444316<br />
</pre><br />
<br />
*POSCAR (of the final state, in directory 03)<br />
<br />
<pre><br />
<br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.500000 0.000000 0.444316<br />
0.756381 0.256381 0.347171<br />
0.243619 0.743619 0.347171<br />
0.756381 0.743619 0.347171<br />
0.243619 0.256381 0.347171<br />
</pre><br />
<br />
4. concatenate the {{FILE|POSCAR}} files of i and f to the file {{FILE|POSCAR1_POSCAR2}}<br />
MIND: <br />
<br />
-- these files must not include the lines with the names of the atoms (vasp.5.2 only) and 'Selective Dynamics',<br />
<br />
-- there must be no blank line between the POSCARS<br />
<br />
-- the block with the velocities of the atoms must be deleted<br />
<br />
-- be careful to check that in {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>j</sub> all atoms are on the same<br />
side of the supercell to avoid that an atom that just jumps across the origin of the cell is dragged through <br />
the cell by the interpolation of the positions.<br />
<br />
5. interpolate the starting geometries of the {{TAG|IMAGES}}, this can be done by using the following script <br />
<br />
interpolatePOSCAR {{FILE|POSCAR1_POSCAR2}}, the interpolated files are written into the respective subdirectories <br />
00 ... 0(N+1)<br />
<br />
<br />
* interpolatePOSCAR<br />
<br />
<pre><br />
file=$1<br />
if [ ! -x $file ]<br />
then<br />
usage: interpolatePOS POSCAR1_POSCAR2<br />
fi<br />
<br />
awk <$file '<br />
BEGIN { rep=4; center=0 }<br />
/center/ { center=1}<br />
/rep/ { rep=$2 }<br />
{ line=line+1<br />
if ( second != 1 ) {<br />
if ( line == 6 ) {<br />
lines = $1 + $2 + $3 + 7<br />
print "found ",lines," ions"<br />
head[line] = $0<br />
} else if ( line < 8 )<br />
head[line] = $0<br />
else<br />
{<br />
x[line-7] = $1 ; y[line-7] = $2 ; z[line-7] = $3<br />
if (line==lines) {<br />
line=0; second=1;<br />
print "first set read"<br />
}<br />
}<br />
} else {<br />
if ( line >= 8 )<br />
{<br />
x2[line-7] = $1; y2[line-7] = $2 ; z2[line-7] = $3 }<br />
if (line==lines) {<br />
print "second set read"<br />
}<br />
}<br />
}<br />
END {<br />
lines=lines-7<br />
for ( line=1; line<=lines ; line ++ ) {<br />
cx1=cx1+ x[line] ; cy1=cy1+ y[line] ; cz1=cz1+ z[line]<br />
cx2=cx2+ x2[line]; cy2=cy2+ y2[line]; cz2=cz2+ z2[line]<br />
}<br />
if (center) {<br />
cx=(cx2-cx1)/lines<br />
cy=(cy2-cy1)/lines<br />
cz=(cz2-cz1)/lines<br />
print "center of mass for second cell will be shifted by",cx,cy,cz<br />
}<br />
<br />
for ( i=0; i<rep ; i++ ) {<br />
file="0" i "/POSCAR"<br />
print "writing to " file<br />
for (line=1; line<=7 ; line++ )<br />
print head[line] >file<br />
for ( line=1; line<=lines ; line ++ ) {<br />
b=i/(rep-1)<br />
a=(rep-1-i)/(rep-1)<br />
dx=a*x[line] + b*(x2[line]-cx)<br />
dy=a*y[line] + b*(y2[line]-cy)<br />
dz=a*z[line] + b*(z2[line]-cz)<br />
<br />
printf " %10.6f %10.6f %10.6f\n",dx,dy,dz >file<br />
}<br />
}<br />
}'<br />
</pre><br />
<br />
NOTE: the total number of steps is explicitely given in line 8 of the script (rep=, rep = {{TAG|IMAGES}}+2). If a dfferent number of {{TAG|IMAGES}} is chosen, this parameter has to be changed. <br />
<br />
6. run vasp: <br />
<br />
MIND: the number of CPUs to be used has to be an integer multiple of {{TAG|IMAGES}}<br />
<br />
7. if convergence is not reached within {{TAG|NSW}} steps, the calculation can be continued by a continuation run, just like for a standard ionic relaxation.<br />
<br />
8. HINT: better convergence is usually achieved if the number of {{TAG|IMAGES}} is rather low (up to 4). If the region close to the transition state is to be<br />
refined, one can do another NEB-calculation, using the ionic configurations of the IMAGES adjacent to the transition state as the new initial and final<br />
states for the follow-up run. <br />
<br />
9: obtain the barrier along diffusion path 00-03 by interpolation (spline)<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Downloads ==<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB.tgz Pt_NEB.tgz],<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB_fast.tgz Pt_NEB_fast.tgz]<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1254Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T15:46:15Z<p>Doris: </p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom Pt@Pt(001) is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward (inputs for a fast, preliminary estimate are given here and in Pt_NEB_fast.tgz, for a more time-consuming, but more accurate setup (larger number of Pt layers, denser k-mesh, higher {{TAG|PREC}} and {{TAG|ENCUT}}) please use the files untarred from Pt_NEB.tgz: <br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
POTIM = 0.5<br />
NSW = 20<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (clean surface)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024<br />
1.0 0.0 0.0<br />
0.0 1.0 0.0<br />
0.0 0.0 3.0<br />
Pt<br />
12<br />
Selective<br />
Direct<br />
0.25 0.25 0.11785 F F F<br />
0.75 0.25 0.11785 F F F<br />
0.25 0.75 0.11785 F F F<br />
0.75 0.75 0.11785 F F F<br />
0.00 0.00 0.23570 F F T<br />
0.00 0.50 0.23570 F F T<br />
0.50 0.00 0.23570 F F T<br />
0.50 0.50 0.23570 F F T<br />
0.25 0.25 0.35355 F F T<br />
0.75 0.25 0.35355 F F T<br />
0.25 0.75 0.35355 F F T<br />
0.75 0.75 0.35355 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), hollow)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt <br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0000000000000000 0.0000000000000000 0.2341409911878811 T T T<br />
0.0000000000000000 0.5000000000000000 0.2344158754007225 T T T<br />
0.5000000000000000 0.0000000000000000 0.2377721273226986 T T T<br />
0.5000000000000000 0.5000000000000000 0.2341409911878811 T T T<br />
0.2500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.2500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.0000000000000000 0.5000000000000000 0.4492270704381683 T T T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), bridge)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0002686432543183 0.0000000000000000 0.2356407813553420 T T T<br />
0.0014220524373488 0.5000000000000000 0.2356795143373628 T T T<br />
0.4997313567456815 0.0000000000000000 0.2356407813553420 T T T<br />
0.4985779475626512 0.5000000000000000 0.2356795143373628 T T T<br />
0.2500000000000000 0.2341977119064422 0.3525947402192897 F T T<br />
0.7500000000000000 0.2518717446753760 0.3518647397661007 T T T<br />
0.2500000000000000 0.7658022880935580 0.3525947402192897 F T T<br />
0.7500000000000000 0.7481282553246233 0.3518647397661007 T T T<br />
0.2500000000000000 0.5000000000000000 0.4716518885541170 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), top<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
-0.0014262288827347 -0.0014262288827347 0.2348121710889565 T T T<br />
-0.0014262288827347 0.5014262288827348 0.2348121710889565 T T T<br />
0.5014262288827348 -0.0014262288827347 0.2348121710889565 T T T<br />
0.5014262288827348 0.5014262288827348 0.2348121710889565 T T T<br />
0.2500000000000000 0.2500000000000000 0.3433443664932221 F F T<br />
0.7500000000000000 0.2500000000000000 0.3546231232810972 T T T<br />
0.2500000000000000 0.7500000000000000 0.3546231232810972 T T T<br />
0.7500000000000000 0.7500000000000000 0.3516055254412989 T T T<br />
0.2500000000000000 0.2500000000000000 0.4861522106341429 F F T<br />
</pre><br />
<br />
the NEB calculation should be done a follows:<br />
<br />
1. run the job from a parent directory containing the files {{FILE|INCAR}}, {{FILE|POTCAR}},{{FILE|KPOINTS}} and the run-script of the job <br />
<br />
2. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in {{FILE|INCAR}}, this corresponds to the parameter {{TAG|IMAGES}}<br />
<br />
3. generate sub-directories 00 (containing the {{FILE|POSCAR}} of the initial geometry i), ... 0(N+1) (containing the {{FILE|POSCAR}} of the final geometry f of the jump). The {{FILE|POSCAR}} files of the intermediate steps, to be interpolated between {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>f</sub><br />
are stored in the directories 01 .. 0N. Calculations are <b>only</b> done for these intermediate steps, the optimization of the geometries is done under the constraint that the relaxing atoms remain on a plane perpendicular to the hypertangent of the diffusion path. All all output files {{FILE|OUTCAR}}, {{FILE|CONTCAR}}, {{FILE|OSZICAR}} .. of the NEB-steps run are written to these subdirectories.<br />
<br />
in the present excercise, the required precision,... is reduced to a minimum (the files are found in Pt_NEB_fast.tar.gz) to save computing time, a<br />
more reliable setup is saved in Pt_NEB.tar.gz)<br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
NSW = 10<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
IMAGES = 2 # 2 intermediate geometries for the NEB<br />
SPRING = -5 # spring constant<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (of the initial state, in directory 00)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000 <br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.256381 0.243619 0.347171<br />
0.743619 0.243619 0.347171<br />
0.256381 0.756381 0.347171<br />
0.743619 0.756381 0.347171<br />
0.000000 0.500000 0.444316<br />
</pre><br />
<br />
*POSCAR (of the final state, in directory 03)<br />
<br />
<pre><br />
<br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.500000 0.000000 0.444316<br />
0.756381 0.256381 0.347171<br />
0.243619 0.743619 0.347171<br />
0.756381 0.743619 0.347171<br />
0.243619 0.256381 0.347171<br />
</pre><br />
<br />
4. concatenate the {{FILE|POSCAR}} files of i and f to the file {{FILE|POSCAR1_POSCAR2}}<br />
MIND: <br />
<br />
-- these files must not include the lines with the names of the atoms (vasp.5.2 only) and 'Selective Dynamics',<br />
<br />
-- there must be no blank line between the POSCARS<br />
<br />
-- the block with the velocities of the atoms must be deleted<br />
<br />
-- be careful to check that in {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>j</sub> all atoms are on the same<br />
side of the supercell to avoid that an atom that just jumps across the origin of the cell is dragged through <br />
the cell by the interpolation of the positions.<br />
<br />
5. interpolate the starting geometries of the {{TAG|IMAGES}}, this can be done by using the following script <br />
<br />
interpolatePOSCAR {{FILE|POSCAR1_POSCAR2}}, the interpolated files are written into the respective subdirectories <br />
00 ... 0(N+1)<br />
<br />
<br />
* interpolatePOSCAR<br />
<br />
<pre><br />
file=$1<br />
if [ ! -x $file ]<br />
then<br />
usage: interpolatePOS POSCAR1_POSCAR2<br />
fi<br />
<br />
awk <$file '<br />
BEGIN { rep=4; center=0 }<br />
/center/ { center=1}<br />
/rep/ { rep=$2 }<br />
{ line=line+1<br />
if ( second != 1 ) {<br />
if ( line == 6 ) {<br />
lines = $1 + $2 + $3 + 7<br />
print "found ",lines," ions"<br />
head[line] = $0<br />
} else if ( line < 8 )<br />
head[line] = $0<br />
else<br />
{<br />
x[line-7] = $1 ; y[line-7] = $2 ; z[line-7] = $3<br />
if (line==lines) {<br />
line=0; second=1;<br />
print "first set read"<br />
}<br />
}<br />
} else {<br />
if ( line >= 8 )<br />
{<br />
x2[line-7] = $1; y2[line-7] = $2 ; z2[line-7] = $3 }<br />
if (line==lines) {<br />
print "second set read"<br />
}<br />
}<br />
}<br />
END {<br />
lines=lines-7<br />
for ( line=1; line<=lines ; line ++ ) {<br />
cx1=cx1+ x[line] ; cy1=cy1+ y[line] ; cz1=cz1+ z[line]<br />
cx2=cx2+ x2[line]; cy2=cy2+ y2[line]; cz2=cz2+ z2[line]<br />
}<br />
if (center) {<br />
cx=(cx2-cx1)/lines<br />
cy=(cy2-cy1)/lines<br />
cz=(cz2-cz1)/lines<br />
print "center of mass for second cell will be shifted by",cx,cy,cz<br />
}<br />
<br />
for ( i=0; i<rep ; i++ ) {<br />
file="0" i "/POSCAR"<br />
print "writing to " file<br />
for (line=1; line<=7 ; line++ )<br />
print head[line] >file<br />
for ( line=1; line<=lines ; line ++ ) {<br />
b=i/(rep-1)<br />
a=(rep-1-i)/(rep-1)<br />
dx=a*x[line] + b*(x2[line]-cx)<br />
dy=a*y[line] + b*(y2[line]-cy)<br />
dz=a*z[line] + b*(z2[line]-cz)<br />
<br />
printf " %10.6f %10.6f %10.6f\n",dx,dy,dz >file<br />
}<br />
}<br />
}'<br />
</pre><br />
<br />
NOTE: the total number of steps is explicitely given in line 8 of the script (rep=, rep = {{TAG|IMAGES}}+2). If a dfferent number of {{TAG|IMAGES}} is chosen, this parameter has to be changed. <br />
<br />
6. run vasp: <br />
<br />
MIND: the number of CPUs to be used has to be an integer multiple of {{TAG|IMAGES}}<br />
<br />
7. if convergence is not reached within {{TAG|NSW}} steps, the calculation can be continued by a continuation run, just like for a standard ionic relaxation.<br />
<br />
8. HINT: better convergence is usually achieved if the number of {{TAG|IMAGES}} is rather low (up to 4). If the region close to the transition state is to be<br />
refined, one can do another NEB-calculation, using the ionic configurations of the IMAGES adjacent to the transition state as the new initial and final<br />
states for the follow-up run. <br />
<br />
9: obtain the barrier along diffusion path 00-03 by interpolation (spline)<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Downloads ==<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB.tgz Pt_NEB.tgz],<br />
[http://www.vasp.at/vasp-workshop/examples/Pt_NEB_fast.tgz Pt_NEB_fast.tgz]<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1249Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T15:40:53Z<p>Doris: </p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom Pt@Pt(001) is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward (inputs for a fast, preliminary estimate are given here and in Pt_NEB_fast.tgz, for a more time-consuming, but more accurate setup (larger number of Pt layers, denser k-mesh, higher {{TAG|PREC}} and {{TAG|ENCUT}}) please use the files untarred from Pt_NEB.tgz: <br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
POTIM = 0.5<br />
NSW = 20<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (clean surface)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024<br />
1.0 0.0 0.0<br />
0.0 1.0 0.0<br />
0.0 0.0 3.0<br />
Pt<br />
12<br />
Selective<br />
Direct<br />
0.25 0.25 0.11785 F F F<br />
0.75 0.25 0.11785 F F F<br />
0.25 0.75 0.11785 F F F<br />
0.75 0.75 0.11785 F F F<br />
0.00 0.00 0.23570 F F T<br />
0.00 0.50 0.23570 F F T<br />
0.50 0.00 0.23570 F F T<br />
0.50 0.50 0.23570 F F T<br />
0.25 0.25 0.35355 F F T<br />
0.75 0.25 0.35355 F F T<br />
0.25 0.75 0.35355 F F T<br />
0.75 0.75 0.35355 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), hollow)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt <br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0000000000000000 0.0000000000000000 0.2341409911878811 T T T<br />
0.0000000000000000 0.5000000000000000 0.2344158754007225 T T T<br />
0.5000000000000000 0.0000000000000000 0.2377721273226986 T T T<br />
0.5000000000000000 0.5000000000000000 0.2341409911878811 T T T<br />
0.2500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.2500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.0000000000000000 0.5000000000000000 0.4492270704381683 T T T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), bridge)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0002686432543183 0.0000000000000000 0.2356407813553420 T T T<br />
0.0014220524373488 0.5000000000000000 0.2356795143373628 T T T<br />
0.4997313567456815 0.0000000000000000 0.2356407813553420 T T T<br />
0.4985779475626512 0.5000000000000000 0.2356795143373628 T T T<br />
0.2500000000000000 0.2341977119064422 0.3525947402192897 F T T<br />
0.7500000000000000 0.2518717446753760 0.3518647397661007 T T T<br />
0.2500000000000000 0.7658022880935580 0.3525947402192897 F T T<br />
0.7500000000000000 0.7481282553246233 0.3518647397661007 T T T<br />
0.2500000000000000 0.5000000000000000 0.4716518885541170 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), top<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
-0.0014262288827347 -0.0014262288827347 0.2348121710889565 T T T<br />
-0.0014262288827347 0.5014262288827348 0.2348121710889565 T T T<br />
0.5014262288827348 -0.0014262288827347 0.2348121710889565 T T T<br />
0.5014262288827348 0.5014262288827348 0.2348121710889565 T T T<br />
0.2500000000000000 0.2500000000000000 0.3433443664932221 F F T<br />
0.7500000000000000 0.2500000000000000 0.3546231232810972 T T T<br />
0.2500000000000000 0.7500000000000000 0.3546231232810972 T T T<br />
0.7500000000000000 0.7500000000000000 0.3516055254412989 T T T<br />
0.2500000000000000 0.2500000000000000 0.4861522106341429 F F T<br />
</pre><br />
<br />
the NEB calculation should be done a follows:<br />
<br />
1. run the job from a parent directory containing the files {{FILE|INCAR}}, {{FILE|POTCAR}},{{FILE|KPOINTS}} and the run-script of the job <br />
<br />
2. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in {{FILE|INCAR}}, this corresponds to the parameter {{TAG|IMAGES}}<br />
<br />
3. generate sub-directories 00 (containing the {{FILE|POSCAR}} of the initial geometry i), ... 0(N+1) (containing the {{FILE|POSCAR}} of the final geometry f of the jump). The {{FILE|POSCAR}} files of the intermediate steps, to be interpolated between {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>f</sub><br />
are stored in the directories 01 .. 0N. Calculations are <b>only</b> done for these intermediate steps, the optimization of the geometries is done under the constraint that the relaxing atoms remain on a plane perpendicular to the hypertangent of the diffusion path. All all output files {{FILE|OUTCAR}}, {{FILE|CONTCAR}}, {{FILE|OSZICAR}} .. of the NEB-steps run are written to these subdirectories.<br />
<br />
in the present excercise, the required precision,... is reduced to a minimum (the files are found in Pt_NEB_fast.tar.gz) to save computing time, a<br />
more reliable setup is saved in Pt_NEB.tar.gz)<br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
NSW = 10<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
IMAGES = 2 # 2 intermediate geometries for the NEB<br />
SPRING = -5 # spring constant<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (of the initial state, in directory 00)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000 <br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.256381 0.243619 0.347171<br />
0.743619 0.243619 0.347171<br />
0.256381 0.756381 0.347171<br />
0.743619 0.756381 0.347171<br />
0.000000 0.500000 0.444316<br />
</pre><br />
<br />
*POSCAR (of the final state, in directory 03)<br />
<br />
<pre><br />
<br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.500000 0.000000 0.444316<br />
0.756381 0.256381 0.347171<br />
0.243619 0.743619 0.347171<br />
0.756381 0.743619 0.347171<br />
0.243619 0.256381 0.347171<br />
</pre><br />
<br />
4. concatenate the {{FILE|POSCAR}} files of i and f to the file {{FILE|POSCAR1_POSCAR2}}<br />
MIND: <br />
<br />
-- these files must not include the lines with the names of the atoms (vasp.5.2 only) and 'Selective Dynamics',<br />
<br />
-- there must be no blank line between the POSCARS<br />
<br />
-- the block with the velocities of the atoms must be deleted<br />
<br />
-- be careful to check that in {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>j</sub> all atoms are on the same<br />
side of the supercell to avoid that an atom that just jumps across the origin of the cell is dragged through <br />
the cell by the interpolation of the positions.<br />
<br />
5. interpolate the starting geometries of the {{TAG|IMAGES}}, this can be done by using the following script <br />
<br />
interpolatePOSCAR {{FILE|POSCAR1_POSCAR2}}, the interpolated files are written into the respective subdirectories <br />
00 ... 0(N+1)<br />
<br />
<br />
* interpolatePOSCAR<br />
<br />
<pre><br />
file=$1<br />
if [ ! -x $file ]<br />
then<br />
usage: interpolatePOS POSCAR1_POSCAR2<br />
fi<br />
<br />
awk <$file '<br />
BEGIN { rep=4; center=0 }<br />
/center/ { center=1}<br />
/rep/ { rep=$2 }<br />
{ line=line+1<br />
if ( second != 1 ) {<br />
if ( line == 6 ) {<br />
lines = $1 + $2 + $3 + 7<br />
print "found ",lines," ions"<br />
head[line] = $0<br />
} else if ( line < 8 )<br />
head[line] = $0<br />
else<br />
{<br />
x[line-7] = $1 ; y[line-7] = $2 ; z[line-7] = $3<br />
if (line==lines) {<br />
line=0; second=1;<br />
print "first set read"<br />
}<br />
}<br />
} else {<br />
if ( line >= 8 )<br />
{<br />
x2[line-7] = $1; y2[line-7] = $2 ; z2[line-7] = $3 }<br />
if (line==lines) {<br />
print "second set read"<br />
}<br />
}<br />
}<br />
END {<br />
lines=lines-7<br />
for ( line=1; line<=lines ; line ++ ) {<br />
cx1=cx1+ x[line] ; cy1=cy1+ y[line] ; cz1=cz1+ z[line]<br />
cx2=cx2+ x2[line]; cy2=cy2+ y2[line]; cz2=cz2+ z2[line]<br />
}<br />
if (center) {<br />
cx=(cx2-cx1)/lines<br />
cy=(cy2-cy1)/lines<br />
cz=(cz2-cz1)/lines<br />
print "center of mass for second cell will be shifted by",cx,cy,cz<br />
}<br />
<br />
for ( i=0; i<rep ; i++ ) {<br />
file="0" i "/POSCAR"<br />
print "writing to " file<br />
for (line=1; line<=7 ; line++ )<br />
print head[line] >file<br />
for ( line=1; line<=lines ; line ++ ) {<br />
b=i/(rep-1)<br />
a=(rep-1-i)/(rep-1)<br />
dx=a*x[line] + b*(x2[line]-cx)<br />
dy=a*y[line] + b*(y2[line]-cy)<br />
dz=a*z[line] + b*(z2[line]-cz)<br />
<br />
printf " %10.6f %10.6f %10.6f\n",dx,dy,dz >file<br />
}<br />
}<br />
}'<br />
</pre><br />
<br />
NOTE: the total number of steps is explicitely given in line 8 of the script (rep=, rep = {{TAG|IMAGES}}+2). If a dfferent number of {{TAG|IMAGES}} is chosen, this parameter has to be changed. <br />
<br />
6. run vasp: <br />
<br />
MIND: the number of CPUs to be used has to be an integer multiple of {{TAG|IMAGES}}<br />
<br />
7. if convergence is not reached within {{TAG|NSW}} steps, the calculation can be continued by a continuation run, just like for a standard ionic relaxation.<br />
<br />
8. HINT: better convergence is usually achieved if the number of {{TAG|IMAGES}} is rather low (up to 4). If the region close to the transition state is to be<br />
refined, one can do another NEB-calculation, using the ionic configurations of the IMAGES adjacent to the transition state as the new initial and final<br />
states for the follow-up run. <br />
<br />
9: obtain the barrier along diffusion path 00-03 by interpolation (spline)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1248Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T15:39:08Z<p>Doris: </p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom Pt@Pt(001) is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward (inputs for a fast, preliminary estimate are given here and in Pt_NEB_fast.tar.gz, for a more time-consuming, but more accurate setup (larger number of Pt layers, denser k-mesh, higher {{TAG|PREC}} and {{TAG|ENCUT}}) please use the files untarred from Pt_NEB.tar.gz: <br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
POTIM = 0.5<br />
NSW = 20<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (clean surface)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024<br />
1.0 0.0 0.0<br />
0.0 1.0 0.0<br />
0.0 0.0 3.0<br />
Pt<br />
12<br />
Selective<br />
Direct<br />
0.25 0.25 0.11785 F F F<br />
0.75 0.25 0.11785 F F F<br />
0.25 0.75 0.11785 F F F<br />
0.75 0.75 0.11785 F F F<br />
0.00 0.00 0.23570 F F T<br />
0.00 0.50 0.23570 F F T<br />
0.50 0.00 0.23570 F F T<br />
0.50 0.50 0.23570 F F T<br />
0.25 0.25 0.35355 F F T<br />
0.75 0.25 0.35355 F F T<br />
0.25 0.75 0.35355 F F T<br />
0.75 0.75 0.35355 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), hollow)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt <br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0000000000000000 0.0000000000000000 0.2341409911878811 T T T<br />
0.0000000000000000 0.5000000000000000 0.2344158754007225 T T T<br />
0.5000000000000000 0.0000000000000000 0.2377721273226986 T T T<br />
0.5000000000000000 0.5000000000000000 0.2341409911878811 T T T<br />
0.2500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.2500000000000000 0.3517982322412672 T T T<br />
0.2500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.7500000000000000 0.7500000000000000 0.3517982322412672 T T T<br />
0.0000000000000000 0.5000000000000000 0.4492270704381683 T T T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), bridge)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.0002686432543183 0.0000000000000000 0.2356407813553420 T T T<br />
0.0014220524373488 0.5000000000000000 0.2356795143373628 T T T<br />
0.4997313567456815 0.0000000000000000 0.2356407813553420 T T T<br />
0.4985779475626512 0.5000000000000000 0.2356795143373628 T T T<br />
0.2500000000000000 0.2341977119064422 0.3525947402192897 F T T<br />
0.7500000000000000 0.2518717446753760 0.3518647397661007 T T T<br />
0.2500000000000000 0.7658022880935580 0.3525947402192897 F T T<br />
0.7500000000000000 0.7481282553246233 0.3518647397661007 T T T<br />
0.2500000000000000 0.5000000000000000 0.4716518885541170 F F T<br />
</pre><br />
<br />
*POSCAR (Pt@Pt(001), top<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
Pt<br />
13<br />
Selective dynamics<br />
Direct<br />
0.2500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.2500000000000000 0.1178499999999971 F F F<br />
0.2500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
0.7500000000000000 0.7500000000000000 0.1178499999999971 F F F<br />
-0.0014262288827347 -0.0014262288827347 0.2348121710889565 T T T<br />
-0.0014262288827347 0.5014262288827348 0.2348121710889565 T T T<br />
0.5014262288827348 -0.0014262288827347 0.2348121710889565 T T T<br />
0.5014262288827348 0.5014262288827348 0.2348121710889565 T T T<br />
0.2500000000000000 0.2500000000000000 0.3433443664932221 F F T<br />
0.7500000000000000 0.2500000000000000 0.3546231232810972 T T T<br />
0.2500000000000000 0.7500000000000000 0.3546231232810972 T T T<br />
0.7500000000000000 0.7500000000000000 0.3516055254412989 T T T<br />
0.2500000000000000 0.2500000000000000 0.4861522106341429 F F T<br />
</pre><br />
<br />
the NEB calculation should be done a follows:<br />
<br />
1. run the job from a parent directory containing the files {{FILE|INCAR}}, {{FILE|POTCAR}},{{FILE|KPOINTS}} and the run-script of the job <br />
<br />
2. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in {{FILE|INCAR}}, this corresponds to the parameter {{TAG|IMAGES}}<br />
<br />
3. generate sub-directories 00 (containing the {{FILE|POSCAR}} of the initial geometry i), ... 0(N+1) (containing the {{FILE|POSCAR}} of the final geometry f of the jump). The {{FILE|POSCAR}} files of the intermediate steps, to be interpolated between {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>f</sub><br />
are stored in the directories 01 .. 0N. Calculations are <b>only</b> done for these intermediate steps, the optimization of the geometries is done under the constraint that the relaxing atoms remain on a plane perpendicular to the hypertangent of the diffusion path. All all output files {{FILE|OUTCAR}}, {{FILE|CONTCAR}}, {{FILE|OSZICAR}} .. of the NEB-steps run are written to these subdirectories.<br />
<br />
in the present excercise, the required precision,... is reduced to a minimum (the files are found in Pt_NEB_fast.tar.gz) to save computing time, a<br />
more reliable setup is saved in Pt_NEB.tar.gz)<br />
<br />
*INCAR<br />
<br />
<pre><br />
System: fcc Pt (001), 3layers<br />
ISTART = 0<br />
EDIFF = 1e-6 # electronic convergence<br />
PREC = Normal<br />
IBRION = 1 # DIIS algorithm<br />
NSW = 10<br />
EDIFFG = -0.01 # max forces: 0.1eV/AA<br />
ELMIN = 5 # at least 5 el. scf steps for each ionic step<br />
IMAGES = 2 # 2 intermediate geometries for the NEB<br />
SPRING = -5 # spring constant<br />
</pre><br />
<br />
*KPOINTS<br />
<br />
<pre><br />
K-Points<br />
0<br />
Gamma<br />
3 3 1<br />
0 0 0<br />
</pre><br />
<br />
*POSCAR (of the initial state, in directory 00)<br />
<br />
<pre><br />
fcc Pt, paw-PBE<br />
5.62024000000000 <br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.256381 0.243619 0.347171<br />
0.743619 0.243619 0.347171<br />
0.256381 0.756381 0.347171<br />
0.743619 0.756381 0.347171<br />
0.000000 0.500000 0.444316<br />
</pre><br />
<br />
*POSCAR (of the final state, in directory 03)<br />
<br />
<pre><br />
<br />
fcc Pt, paw-PBE<br />
5.62024000000000<br />
1.0000000000000000 0.0000000000000000 0.0000000000000000<br />
0.0000000000000000 1.0000000000000000 0.0000000000000000<br />
0.0000000000000000 0.0000000000000000 3.0000000000000000<br />
13<br />
Direct<br />
0.250000 0.250000 0.117850<br />
0.750000 0.250000 0.117850<br />
0.250000 0.750000 0.117850<br />
0.750000 0.750000 0.117850<br />
0.000000 0.000000 0.230682<br />
0.000000 0.500000 0.230971<br />
0.500000 0.000000 0.234757<br />
0.500000 0.500000 0.230682<br />
0.500000 0.000000 0.444316<br />
0.756381 0.256381 0.347171<br />
0.243619 0.743619 0.347171<br />
0.756381 0.743619 0.347171<br />
0.243619 0.256381 0.347171<br />
</pre><br />
<br />
4. concatenate the {{FILE|POSCAR}} files of i and f to the file {{FILE|POSCAR1_POSCAR2}}<br />
MIND: <br />
<br />
-- these files must not include the lines with the names of the atoms (vasp.5.2 only) and 'Selective Dynamics',<br />
<br />
-- there must be no blank line between the POSCARS<br />
<br />
-- the block with the velocities of the atoms must be deleted<br />
<br />
-- be careful to check that in {{FILE|POSCAR}}<sub>i</sub> and {{FILE|POSCAR}}<sub>j</sub> all atoms are on the same<br />
side of the supercell to avoid that an atom that just jumps across the origin of the cell is dragged through <br />
the cell by the interpolation of the positions.<br />
<br />
5. interpolate the starting geometries of the {{TAG|IMAGES}}, this can be done by using the following script <br />
<br />
interpolatePOSCAR {{FILE|POSCAR1_POSCAR2}}, the interpolated files are written into the respective subdirectories <br />
00 ... 0(N+1)<br />
<br />
<br />
* interpolatePOSCAR<br />
<br />
<pre><br />
file=$1<br />
if [ ! -x $file ]<br />
then<br />
usage: interpolatePOS POSCAR1_POSCAR2<br />
fi<br />
<br />
awk <$file '<br />
BEGIN { rep=4; center=0 }<br />
/center/ { center=1}<br />
/rep/ { rep=$2 }<br />
{ line=line+1<br />
if ( second != 1 ) {<br />
if ( line == 6 ) {<br />
lines = $1 + $2 + $3 + 7<br />
print "found ",lines," ions"<br />
head[line] = $0<br />
} else if ( line < 8 )<br />
head[line] = $0<br />
else<br />
{<br />
x[line-7] = $1 ; y[line-7] = $2 ; z[line-7] = $3<br />
if (line==lines) {<br />
line=0; second=1;<br />
print "first set read"<br />
}<br />
}<br />
} else {<br />
if ( line >= 8 )<br />
{<br />
x2[line-7] = $1; y2[line-7] = $2 ; z2[line-7] = $3 }<br />
if (line==lines) {<br />
print "second set read"<br />
}<br />
}<br />
}<br />
END {<br />
lines=lines-7<br />
for ( line=1; line<=lines ; line ++ ) {<br />
cx1=cx1+ x[line] ; cy1=cy1+ y[line] ; cz1=cz1+ z[line]<br />
cx2=cx2+ x2[line]; cy2=cy2+ y2[line]; cz2=cz2+ z2[line]<br />
}<br />
if (center) {<br />
cx=(cx2-cx1)/lines<br />
cy=(cy2-cy1)/lines<br />
cz=(cz2-cz1)/lines<br />
print "center of mass for second cell will be shifted by",cx,cy,cz<br />
}<br />
<br />
for ( i=0; i<rep ; i++ ) {<br />
file="0" i "/POSCAR"<br />
print "writing to " file<br />
for (line=1; line<=7 ; line++ )<br />
print head[line] >file<br />
for ( line=1; line<=lines ; line ++ ) {<br />
b=i/(rep-1)<br />
a=(rep-1-i)/(rep-1)<br />
dx=a*x[line] + b*(x2[line]-cx)<br />
dy=a*y[line] + b*(y2[line]-cy)<br />
dz=a*z[line] + b*(z2[line]-cz)<br />
<br />
printf " %10.6f %10.6f %10.6f\n",dx,dy,dz >file<br />
}<br />
}<br />
}'<br />
</pre><br />
<br />
NOTE: the total number of steps is explicitely given in line 8 of the script (rep=, rep = {{TAG|IMAGES}}+2). If a dfferent number of {{TAG|IMAGES}} is chosen, this parameter has to be changed. <br />
<br />
6. run vasp: <br />
<br />
MIND: the number of CPUs to be used has to be an integer multiple of {{TAG|IMAGES}}<br />
<br />
7. if convergence is not reached within {{TAG|NSW}} steps, the calculation can be continued by a continuation run, just like for a standard ionic relaxation.<br />
<br />
8. HINT: better convergence is usually achieved if the number of {{TAG|IMAGES}} is rather low (up to 4). If the region close to the transition state is to be<br />
refined, one can do another NEB-calculation, using the ionic configurations of the IMAGES adjacent to the transition state as the new initial and final<br />
states for the follow-up run. <br />
<br />
9: obtain the barrier along diffusion path 00-03 by interpolation (spline)<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1219Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T13:33:26Z<p>Doris: </p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier <ref name="kellog:prl64:3143"/><br />
<br />
The calculation of the barrier heights involves the following steps:<br />
<br />
1. calculation of the bulk a<sub>0</sub> of Pt for the chosen functional<br />
<br />
2. a clean Pt (001) surface, with a 2D supercell of -at minimum- (2x2) reconstruction<br />
<br />
3. the energies of the surface including the Pt-adatom in h, b, and t position<br />
<br />
4. a Nudged Elastic Band (NEB) calculation <ref name="NEB"/> for the proposed collective jump mechanism<br />
<br />
steps 1-3 are straightforward, therefore only the files and the procedure for the NEB calculation are given here:<br />
<br />
1. consider how many intermediate geometries (N) should be chosen between the initial and the final state of the jump<br />
in INCAR, this corresponds to the tag <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== References ==<br />
<references><br />
<ref name="kellog:prl64:3143"> G.L.Kellogg and Peter J.Feibelman, Phys. Rev. Lett. <b>64</b> (26), 3143 (1990) </ref><br />
<ref name="NEB">G. Mills, H. Jonsson and G. K. Schenter, Surface Science, <b>324</b>, 305 (1995); H. Jonsson, G. Mills and K. W. Jacobsen,<br />
`Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions',<br />
in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998) </ref></div>Dorishttps://www.vasp.at/wiki/index.php?title=Collective_jumps_of_a_Pt_adatom_on_fcc-Pt_(001):_Nudged_Elastic_Band_Calculation&diff=1218Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation2012-06-08T13:07:18Z<p>Doris: Created page with 'Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom is the hollow (h) position. Simple mo…'</p>
<hr />
<div>Description: calculate the energy barrier for the self-diffusion (of a Pt-adatom) on Pt (001): The most stable adsorption site of the adatom is the hollow (h) position. Simple models of the diffusion of the adatom from h to the neighboring h site include two diffusion paths: hollow-top-hollow (hth, eg along [1-10]) or hollow-bridge-hollow (hbh, eg along [100]). A collective jump mechanism involving 2 Pt atoms diffusing along [1-10] is proposed to be the diffusion mechanism with the lowest energy barrier .</div>Dorishttps://www.vasp.at/wiki/index.php?title=SPRING&diff=335SPRING2011-02-11T16:38:51Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|SPRING|[integer]|-5}}<br />
<br />
Description: {{TAG|SPRING}} gives the ''spring constant'' between the images as used in the elastic band method <br />
<br />
----<br />
{{TAG|SPRING}} has to be set together with {{TAG|IMAGES}} if the elastic band method is used to calculate energy barriers between two <br />
ionic configurations of a system.<br />
<br />
For {{TAG|SPRING}} = 0, each image is only allowed<br />
to move into the direction perpendicular to the current<br />
hyper-tangent, which is calculated as the normal vector<br />
between two neighboring images.<br />
This algorithm keeps the distance between the images<br />
constant to ''first order''. It is therefore possible to start<br />
with a dense image spacing around the saddle point to obtain<br />
a finer resolution around this point.<br />
<br />
The nudged elastic band method<ref name="jons95"/><ref name="jons98"/><br />
is applied when {{TAG|SPRING}} is set to a negative value e.g.<br />
{{TAG|SPRING}}= -5<br />
This is also the recommended setting.<br />
Compared to the previous case, additional tangential springs<br />
are introduced to keep the images equidistant<br />
during the relaxation (remember the constraint is only<br />
conserved to first order otherwise). Do not use too large values,<br />
because this can slow down convergence. The default value<br />
usually works quite reliably.<br />
<br />
One problem of the nudged elastic band method is<br />
that the constraint (i.e movements only<br />
in the hyper-plane perpendicular to the current tangent) is<br />
non linear. Therefore, the CG algorithm usually fails<br />
to converge, and we recommended to use<br />
the {{TAG|RMM-DIIS}} algorithm ({{TAG|IBRION}}=1) or the quick-min algorithm ({{TAG|IBRION}}=3).<br />
Additionally,<br />
the non-linear constraint (equidistant images) tends to be violated<br />
significantly during the first few steps (it is only enforced to first order).<br />
If this problem is<br />
encountered, a very low dimensionality parameter ({{TAG|IBRION}}=1, {{TAG|NFREE}}=2)<br />
should be applied in the first we steps, or a steepest<br />
descent minimization without line optimization ({{TAG|IBRION}}=3, {{TAG|SMASS}}=2).<br />
should be used, to pre-converge the images.<br />
<br />
== Related Tags and Sections ==<br />
{{TAG|IMAGES}},<br />
{{TAG|IBRION}},<br />
{{TAG|NFREE}},<br />
{{TAG|SMASS}}<br />
<br />
== References ==<br />
<references><br />
<ref name="jons95">[http://dx.doi.org/10.1016/0039-6028(94)00731-4 G. Mills, H. Jonsson and G. K. Schenter, Surface Science, 324, 305 (1995).]</ref><br />
<ref name="jons98">H. Jonsson, G. Mills and K. W. Jacobsen, ''Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions'', in ''Classical and Quantum Dynamics in Condensed Phase Simulations'', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998).</ref><br />
</references><br />
----<br />
<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]][[Category:Transition States]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=POTIM&diff=331POTIM2011-02-11T16:19:13Z<p>Doris: Created page with '{{TAGDEF|POTIM|[real]}} {{DEF|POTIM|none,| ''must'' be set if {{TAG|IBRION}}{{=}} 0 (MD)|0.5| if {{TAG|IBRION}}{{=}} 1,2,3 (ionic relaxation) and 5 (up to VASP.4.6)|0.015|for {{…'</p>
<hr />
<div>{{TAGDEF|POTIM|[real]}}<br />
<br />
{{DEF|POTIM|none,| ''must'' be set if {{TAG|IBRION}}{{=}} 0 (MD)|0.5| if {{TAG|IBRION}}{{=}} 1,2,3 (ionic relaxation) and 5 (up to VASP.4.6)|0.015|for {{TAG|IBRION}}{{=}}5 (up from VASP.5.1)}}<br />
<br />
Description: time (MD) or step width scaling (ionic relaxations) constant <br />
<br />
----<br />
<span><br />
{{TAG|IBRION}} = 0 :<br />
:{{TAG|POTIM}} gives the time step in all ab-initio Molecular Dynamics runs, it ''has'' to be supplied therefore, otherwise VASP crashes immediately after having started.<br />
</span><br />
<span><br />
{{TAG|IBRION}} =1,2,3 <br />
:in all minimization algorithms (quasi-Newton, conjugate gradient, and damped molecular dynamics) {{TAG|POTIM}} serves as a scaling constant for the step widths. Especially the Quasi-Newton algorithm is sensitive to the choice of this parameter<br />
</span><br />
<span><br />
{{TAG|IBRION}} = 5 (6)<br />
:in frozen phonon calculations, {{TAG|POTIM}} gives the width of the displacement of each ion to calculate the Hessian Matrix. <br />
:'''VASP.4.6''' and older releases: {{TAG|POTIM}} has to be small enough to ensure that the displacements are within the harmonic limit. The vibrational frequencies using the frozen phonon approach are based on the harmonic approximation.<br />
:'''VASP.5.1''' and newer releases: if the supplied value for {{TAG|POTIM}} is unreasonably large, {{TAG|POTIM}} is automatically reset to 0.015&Aring;<br />
</span><br />
----<br />
== Related Tags and Sections ==<br />
{{TAG|IBRION}}, ({{TAG|NFREEE}})<br />
<br />
[[The_VASP_Manual|Contents]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=NFREE&diff=325NFREE2011-02-11T15:53:11Z<p>Doris: Created page with '{{TAGDEF|NFREE|[integer]}} {{DEF|NFREE|1|if {{TAG|IBRION}}{{=}}2|0|else|}} Description: depending on {{TAG|IBRION}}: gives the number of remembered steps in the history of ioni…'</p>
<hr />
<div>{{TAGDEF|NFREE|[integer]}}<br />
<br />
{{DEF|NFREE|1|if {{TAG|IBRION}}{{=}}2|0|else|}}<br />
<br />
Description: depending on {{TAG|IBRION}}: gives the number of remembered steps in the history of ionic convergence runs, or the number of ionic displacements in frozen phonon calculations <br />
----<br />
<span><br />
*'''{{TAG|IBRION}} = 1''' (quasi-Newton algorithm for ionic relaxation): <br />
<br />
:(i) If {{TAG|NFREE}} '''is''' set, only up to {{TAG|NFREE}} ionic steps are kept in the iteration history (the rank of the approximate Hessian matrix is not larger than {{TAG|NFREE}}).<br />
<br />
:(ii) If {{TAG|NFREE}} '''is not''' specified, the criterion whether information is removed from the iteration history is based on the eigenvalue spectrum of the inverse Hessian matrix: if one eigenvalue of the inverse Hessian matrix is larger than 8, information from previous steps is discarded. For complex problems {{TAG|NFREE}} can usually be set to a rather large value (i.e. 10-20), however systems of low dimensionality require a careful setting of {{TAG|NFREE}} (or preferably an exact counting of the number of degrees of freedom). To increase {{TAG|NFREE}} beyond 20 rarely improves convergence. If {{TAG|NFREE}} is set to too large, the {{TAG|RMM-DIIS}} algorithm might diverge.<br />
</span><br />
<span><br />
*'''{{TAG|IBRION}} = 5''' (from VASP.4.5) or '''6''' (from VASP.5.1): frozen phonon approach to calculate the zone-center vibrational frequencies of a system.<br />
:{{TAG|NFREE}} determines how many displacements are used for each direction and ion. The step size has to be given in {{TAG|INCAR}}, by the tag {{TAG|POTIM}}. Displacements should be small enough to ensure that the harmonic approximation is safely fulfilled. If too large values are supplied in the input file, it is defaulted to 0.015 &Aring; up from VASP.5.1 (but ''not'' in all earlier releases). Expertise shows that this is a very reasonable compromise.<br />
<br />
:{{TAG|NFREE}} = 2 uses central difference, ''i.e'' each ion is displaced in each direction by a small positive and negative displacement<br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{x} </math>, <br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{y} </math>,<br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{z} </math>,<br />
<br />
:For {{TAG|NFREE}} = 4, four displacements are used<br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{x} </math> and <math>\pm</math> 2 * {{TAG|POTIM}} * <math>\hat{x}</math>,<br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{y} </math> and <math>\pm</math> 2 * {{TAG|POTIM}} * <math>\hat{x}</math>,<br />
<br />
<math>\pm</math> {{TAG|POTIM}} * <math>\hat{z} </math> and <math>\pm</math> 2 * {{TAG|POTIM}} * <math>\hat{x}</math>,<br />
<br />
<br />
:For {{TAG|NFREE}}=1, only a single displacement is applied (it is strongly recommend to avoid {{TAG|NFREE}}=1).<br />
<br />
----<br />
== Related Tags and Sections ==<br />
{{TAG|IBRION}},<br />
{{TAG|POTIM}}<br />
<br />
[[The_VASP_Manual|Contents]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=SPRING&diff=308SPRING2011-02-11T14:46:59Z<p>Doris: </p>
<hr />
<div>{{TAGDEF|SPRING|[integer]|-5}}<br />
<br />
Description: {{TAG|SPRING}} gives the ''spring constant'' between the images as used in the elastic band method <br />
<br />
----<br />
{{TAG|SPRING}} has to be set together with {{TAG|IMAGES}} if the elastic band method is used to calculate energy barriers between two <br />
ionic configurations of a system.<br />
<br />
For {{TAG|SPRING}} = 0, each image is only allowed<br />
to move into the direction perpendicular to the current<br />
hyper-tangent, which is calculated as the normal vector<br />
between two neighboring images.<br />
This algorithm keeps the distance between the images<br />
constant to ''first order''. It is therefore possible to start<br />
with a dense image spacing around the saddle point to obtain<br />
a finer resolution around this point.<br />
<br />
The nudged elastic band method <ref name="jons95"/><ref name="jons98"/><br />
is applied when {{TAG|SPRING}} is set to a negative value e.g.<br />
SPRING = -5<br />
This is also the recommended setting.<br />
Compared to the previous case, additional tangential springs<br />
are introduced to keep the images equidistant<br />
during the relaxation (remember the constraint is only<br />
conserved to first order otherwise). Do not use too large values,<br />
because this can slow down convergence. The default value<br />
usually works quite reliably.<br />
<br />
One problem of the nudged elastic band method is<br />
that the constraint (i.e movements only<br />
in the hyper-plane perpendicular to the current tangent) is<br />
non linear. Therefore, the CG algorithm usually fails<br />
to converge, and we recommended to use<br />
the {{TAG|RMM-DIIS}} algorithm ({{TAG|IBRION}}=1) or the quick-min algorithm ({TAG|IBRION}}=3).<br />
Additionally,<br />
the non-linear constraint (equidistant images) tends to be violated<br />
significantly during the first few steps (it is only enforced to first order).<br />
If this problem is<br />
encountered, a very low dimensionality parameter ({{TAG|IBRION}}=1, {{TAG|NFREE}}=2)<br />
should be applied in the first we steps, or a steepest<br />
descent minimization without line optimization ({{TAG|IBRION}}=3, {{TAG|SMASS}}=2).<br />
should be used, to pre-converge the images.<br />
<br />
== References ==<br />
<references><br />
<ref name="jons95">G. Mills, H. Jonsson and G. K. Schenter, Surface<br />
Science, 324, 305 (1995)</ref><br />
<ref name="jons98">H. Jonsson, G. Mills and K. W. Jacobsen,<br />
''Nudged Elastic Band Method for Finding Minimum Energy Paths of<br />
Transitions'',<br />
in ''Classical and Quantum Dynamics in Condensed Phase Simulations'',<br />
ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998)</ref><br />
</references><br />
----<br />
== Related Tags and Sections ==<br />
{{TAG|IMAGES}}<br />
{{TAG|IBRION}}<br />
{{TAG|NFREE}}<br />
{{TAG|SMASS}}<br />
<br />
[[The_VASP_Manual|Contents]]<br />
<br />
[[Category:INCAR]][[Category:Elastic Band Method]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=SPRING&diff=307SPRING2011-02-11T14:44:00Z<p>Doris: Created page with '{{TAGDEF|SPRING|[integer]|-5}} Description: {{TAG|SPRING}} gives the ''spring constant'' between the images as used in the elastic band method ---- {{TAG|SPRING}} has to be s…'</p>
<hr />
<div>{{TAGDEF|SPRING|[integer]|-5}}<br />
<br />
Description: {{TAG|SPRING}} gives the ''spring constant'' between the images as used in the elastic band method <br />
<br />
----<br />
{{TAG|SPRING}} has to be set together with {{TAG|IMAGES}} if the elastic band method is used to calculate energy barriers between two <br />
ionic configurations of a system.<br />
<br />
For {{TAG|SPRING}} = 0, each image is only allowed<br />
to move into the direction perpendicular to the current<br />
hyper-tangent, which is calculated as the normal vector<br />
between two neighboring images.<br />
This algorithm keeps the distance between the images<br />
constant to ''first order''. It is therefore possible to start<br />
with a dense image spacing around the saddle point to obtain<br />
a finer resolution around this point.<br />
<br />
The nudged elastic band method <ref name="jons95"/><ref name="jons98"/><br />
is applied when {{TAG|SPRING}} is set to a negative value e.g.<br />
SPRING = -5<br />
This is also the recommended setting.<br />
Compared to the previous case, additional tangential springs<br />
are introduced to keep the images equidistant<br />
during the relaxation (remember the constraint is only<br />
conserved to first order otherwise). Do not use too large values,<br />
because this can slow down convergence. The default value<br />
usually works quite reliably.<br />
<br />
== References ==<br />
<references><br />
<ref name="jons95">G. Mills, H. Jonsson and G. K. Schenter, Surface<br />
Science, 324, 305 (1995)</ref><br />
<ref name="jons98">H. Jonsson, G. Mills and K. W. Jacobsen,<br />
''Nudged Elastic Band Method for Finding Minimum Energy Paths of<br />
Transitions'',<br />
in ''Classical and Quantum Dynamics in Condensed Phase Simulations'',<br />
ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998)</ref><br />
</references><br />
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== Related Tags and Sections ==<br />
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[[Category:INCAR]][[Category:Elastic Band Method]]</div>Dorishttps://www.vasp.at/wiki/index.php?title=LCHARG&diff=305LCHARG2011-02-11T13:38:39Z<p>Doris: Created page with '{{TAGDEF|LCHARG|[logical]|.True.}} Description: {{TAG|LCHARG}} determines whether the charge densities (files {{TAG|CHGCAR}} and {{TAG|CHG}}) are written. == Related Tags and S…'</p>
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<div>{{TAGDEF|LCHARG|[logical]|.True.}}<br />
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<div>{{TAGDEF|LWAVE|[logical]|.True.}}<br />
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Description: {{TAG|LWAVE}} determines whether the wavefunctions (file {{TAG|WAVECAR}}) are written at the end of a run<br />
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