http://w.atwiki.jp/abinit/ abinit @ ウィキ ja 2010-04-05T03:52:25+09:00 1270407145 https://w.atwiki.jp/abinit/pages/18.html *圧力温度制御 まずは精度を気にせずに温度圧力制御下での構造最適化を行いたい。 2010-04-05T03:52:25+09:00 1270407145 https://w.atwiki.jp/abinit/pages/15.html *VARBAS 基本的な変数 **acell セルの大きさ(by Bohr, 1Bohr=0.5291772108Å, 1Å=1.889726Bohr) 基底ベクトルの長さを表していて、３つで１セット。 **ecut エネルギーカットオフ(by Bohr) 与えられたK点での平面波の波数をコントロールする運動エネルギーのカットオフ。 デフォルトの単位はHartree。 収束の計算には大きい値を用いるほうが良い。 **iscf 自己撞着場サイクルを決める整数。 # =1 => get the largest eigenvalue of the SCF cycle (DEVELOP option, used with irdwfk=1 or irdwfq=1) # =2 => SCF cycle, simple mixing of the potential # =3 => SCF cycle, Anderson mixing of the potential # =4 => SCF cycle, Anderson mixing of the potential based on the two previous iterations # =5 => SCF cycle, CG based on the minim. of the energy with respect to the potential # =7 => SCF cycle, Pulay mixing of the potential based on the npulayit previous iterations # =12 => SCF cycle, simple mixing of the density # =13 => SCF cycle, Anderson mixing of the density # =14 => SCF cycle, Anderson mixing of the density based on the two previous iterations # =15 => SCF cycle, CG based on the minim. of the energy with respect to the density # =17 => SCF cycle, Pulay mixing of the density based on the npulayit previous iterations そのまま引用。デフォルトは7。 **ixc 0=> NO xc; 1=> LDA or LSD, Teter Pade parametrization (4/93, published in S. Goedecker, M. Teter, J. Huetter, Phys.Rev.B54, 1703 (1996)), which reproduces Perdew-Wang (which reproduces Ceperley-Alder!). 2=> LDA, Perdew-Zunger-Ceperley-Alder (no spin-polarization) 3=> LDA, old Teter rational polynomial parametrization (4/91) fit to Ceperley-Alder data (no spin-polarization) 4=> LDA, Wigner functional (no spin-polarization) 5=> LDA, Hedin-Lundqvist functional (no spin-polarization) 6=> LDA, "X-alpha" functional (no spin-polarization) 7=> LDA or LSD, Perdew-Wang 92 functional 8=> LDA or LSD, x-only part of the Perdew-Wang 92 functional 9=> LDA or LSD, x- and RPA correlation part of the Perdew-Wang 92 functional 11=> GGA, Perdew-Burke-Ernzerhof GGA functional 12=> GGA, x-only part of Perdew-Burke-Ernzerhof GGA functional 13=> GGA potential of van Leeuwen-Baerends, while for energy, Perdew-Wang 92 functional 14=> GGA, revPBE of Y. Zhang and W. Yang, Phys. Rev. Lett. 80, 890 (1998) 15=> GGA, RPBE of B. Hammer, L.B. Hansen and J.K. Norskov, Phys. Rev. B 59, 7413 (1999) 16=> GGA, HTCH93 of F.A. Hamprecht, A.J. Cohen, D.J. Tozer, N.C. Handy, J. Chem. Phys. 109, 6264 (1998) 17=> GGA, HTCH120 of A.D. Boese, N.L. Doltsinis, N.C. Handy, and M. Sprik, J. Chem. Phys 112, 1670 (1998) - The usual HCTH functional. 18=> (NOT AVAILABLE : tentative assignment, for planning purposes) GGA, BLYP. 19=> (NOT AVAILABLE : tentative assignment, for planning purposes) GGA, BP. 20=> Fermi-Amaldi xc ( -1/N Hartree energy, where N is the number of electrons per cell ; G=0 is not taken into account however), for TDDFT tests. No spin-pol. Does not work for RF. 21=> same as 20, except that the xc-kernel is the LDA (ixc=1) one, for TDDFT tests. 22=> same as 20, except that the xc-kernel is the Burke-Petersilka-Gross hybrid, for TDDFT tests. 23=> GGA of Z. Wu and R.E. Cohen, Phys. Rev. 73, 235116 (2006). 26=> GGA, HTCH147 of A.D. Boese, N.L. Doltsinis, N.C. Handy, and M. Sprik, J. Chem. Phys 112, 1670 (1998). 27=> GGA, HTCH407 of A.D. Boese, and N.C. Handy, J. Chem. Phys 114, 5497 (2001). 28=> (NOT AVAILABLE : tentative assignment, for planning purposes) GGA, OLYP. 30=> (tentative assignment, for testing purposes) X-only functional, from the Nanoquanta libxc, developed by Miguel Marques 31=> (tentative assignment, for testing purposes) X+ VWN C functional, from the Nanoquanta libxc, developed by Miguel Marques 32=> (tentative assignment, for testing purposes) X+ PZ C functional, from the Nanoquanta libxc, developed by Miguel Marques 33=> (tentative assignment, for testing purposes) X+ PW C functional, from the Nanoquanta libxc, developed by Miguel Marques 34=> (tentative assignment, for testing purposes) X+ AMGB C functional, from the Nanoquanta libxc, developed by Miguel Marques **kpt k点。デフォルトは原点。 ブリルアンゾーン中で対称性の良い点を特にk点と呼んでいる。 **kptopt k点の最適化。デフォルトは0 0=> read directly nkpt, kpt, kptnrm and wtk. 1=> rely on ngkpt or kptrlatt, as well as on nshiftk and shiftk to set up the k points. Take fully into account the symmetry to generate the k points in the Irreducible Brillouin Zone only. (This is the usual mode for GS calculations) 2=> rely on ngkpt or kptrlatt, as well as on nshiftk and shiftk to set up the k points. Take into account only the time-reversal symmetry : k points will be generated in half the Brillouin zone. (This is to be used when preparing or executing a RF calculation at q=(0 0 0) ) 3=> rely on ngkpt or kptrlatt, as well as on nshiftk and shiftk to set up the k points. Do not take into account any symmetry : k points will be generated in the full Brillouin zone. (This is to be used when preparing or executing a RF calculation at non-zero q ) 4=> rely on ngkpt or kptrlatt, as well as on nshiftk and shiftk to set up the k points. Take into account all the symmetries EXCEPT the time-reversal symmetry to generate the k points in the Irreducible Brillouin Zone. This has to be used when performing PAW calculations including spin-orbit coupling (pawspnorb/=0) A negative value => rely on kptbounds, and ndivk to set up a band structure calculation along different lines (allowed only for iscf==-2). The absolute value of kptopt gives the number of segments of the band structure. **nband 電子が入る可能性のあるエネルギーバンドの最大値。 (この理解が正しいかどうかは怪しい） **ngkpt サンプリングするｋ点をコントロールしている、基本グリッドの数。基底ベクトル方向で３セットの値を必要とする。 2×2×2の格子点が欲しければ ngkpt 2 2 2 となる。 **nkpt ngkptから導かれるサンプリングするk点の数。 **nshiftk **nstep SCFサイクルのステップの数。 デフォルトは30。 **ntypat 元素の数。 **occopt **rprim セルのベクトルの方向。３個の３次元ベクトルが必要。 **shiftk **toldfe **toldff **typat 元素の種類。znuclで指定した元素番号の並び順で1,2,3…となっている。 **xangst Åでの直交系での初期原子座標。 **xcart Bohrでの直交系での初期原子座標。 **xred セルの基本ベクトルを１とした場合の初期原子座標。 **znucl 計算する元素の原子番号。 2010-04-04T16:20:10+09:00 1270365610 https://w.atwiki.jp/abinit/pages/19.html *VARGS 基底状態計算のための変数 **tsmear 単位はHartree デフォルトは0.04で、Alのような自由電子金属でも0.04を用いることができる。 d軌道電子を持つ金属では0.01を用いる。 2010-04-03T20:09:25+09:00 1270292965 https://w.atwiki.jp/abinit/pages/17.html *チュートリアル **abinit.orgにある正統なチュートリアル [[lesson1]] [[lesson2]] [[lesson3]] [[lesson4]] **個人的に気になる温度圧力条件下での構造最適化 ***1,[[圧力温度制御]] ***2,[[収束と結果の信頼性]] 2010-04-03T19:18:39+09:00 1270289919 https://w.atwiki.jp/abinit/pages/16.html *VARRLX 構造緩和、構造最適化のための変数 **dtion １ステップの時間。単位は(h/2πHa)=0.02418884fs。 デフォルトは100。 **ionmove 0=> do not move ions (イオンを動かさない） 1=> move atoms using molecular dynamics with optional viscous damping (friction linearly proportional to velocity). The viscous damping is controlled by the parameter "vis". If actual undamped molecular dynamics is desired, set vis to 0. The implemented algorithm is the generalisation of the Numerov technique (6th order), but is NOT invariant upon time-reversal, so that the energy is not conserved. The value ionmov=6 will usually be preferred, although the algorithm that is implemented is lower-order. The time step is governed by dtion. opcell/=0 is not available 2=> conduct structural optimization using the Broyden-Fletcher-Goldfarb-Shanno minimization (BFGS). This is much more efficient for structural optimization than viscous damping, when there are less than let's say 10 degrees of freedom to optimize. 3=> conduct structural optimization using the Broyden-Fletcher-Goldfarb-Shanno minimization (BFGS), modified to take into account the total energy as well as the gradients (as in usual BFGS). See the paper by Schlegel, J. Comp. Chem. 3, 214 (1982). Might be better than ionmov=2 for few degrees of freedom (less than 3 or 4) 4=> conjugate gradient algorithm for simultaneous optimization of potential and ionic degrees of freedom. It can be used with iscf=2 and iscf=5 or 6 (WARNING : this is under development, and does not work very well in many cases). optcell/=0 is not available. 5=> Simple relaxation of ionic positions according to (converged) forces. Equivalent to ionmov=1 with zero masses, albeit the relaxation coefficient is not vis, but iprcfc. optcell/=0 is not available. 6=> Molecular dynamics using the Verlet algorithm, see Allen & Tildesley "Computer simulation of liquids" 1987, p 81. Although partly coded, optcell/=0 is not available. The only related parameter is the time step (dtion). 7=> Quenched Molecular dynamics using the Verlet algorithm, and stopping each atom for which the scalar product of velocity and force is negative. Although partly coded, optcell/=0 is not available. The only related parameter is the time step (dtion). The goal is not to produce a realistic dynamics, but to go as fast as possible to the minimum. For this purpose, it is advised to set all the masses to the same value (for example, use the Carbon mass, i.e. set amu to 12 for all type of atoms). 8=> Molecular dynamics with Nose-Hoover thermostat, using the Verlet algorithm. Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the thermostat mass (noseinert). 9=> Langevin molecular dynamics. Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the friction coefficient (friction). 12=> Isokinetic ensemble molecular dynamics. The equation of motion of the ions in contact with a thermostat are solved with the algorithm proposed by Zhang [J. Chem. Phys. 106, 6102 (1997)], as worked out by Minary et al [J. Chem. Phys. 188, 2510 (2003)]. The conservation of the kinetic energy is obtained within machine precision, at each step. Although partly coded, optcell/=0 is not available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), and the friction coefficient (friction). 13=> Isothermal/isenthalpic ensemble. The equation of motion of the ions in contact with a thermostat and a barostat are solved with the algorithm proposed by Martyna, Tuckermann Tobias and Klein [Mol. Phys., 1996, p. 1117]. optcell/=0 is available. Related parameters : the time step (dtion), the initial temperature (mditemp), the final temperature (mdftemp), the number of thermostats (nnos), and the masses of thermostats (qmass). If optcell=1 or 2, the mass of the barostat (bmass) must be given in addition. 14=> simple molecular dynamics with a symplectic algorithm proposed by S.Blanes and P.C.Moans [called SRKNa14 in Practical symplectic partitioned Runge--Kutta and Runge--Kutta--Nyström methods, Journal of Computational and Applied Mathematics archive, volume 142, issue 2 (May 2002), pages 313 - 330] of the kind first published by H. Yoshida [Construction of higher order symplectic integrators, Physics Letters A, volume 150, number 5 to 7, pages 262 - 268]. This algorithm requires at least 14 evaluation of the forces (actually 15 are done within Abinit) per time step. At this cost it usually gives much better energy conservation than the verlet algorithm (ionmov 6) for a 30 times bigger value of dtion. Notice that the potential energy of the initial atomic configuration is never evaluated using this algorithm. Option optcell/=0 is not available. **mdftemp MD温度の目標値。単位はK。 **mditemp MD温度の初期値。単位はK。 **optcell optcell=0 : modify nuclear positions, since ionmov=2, but no cell shape and dimension optimisation. optcell=1 : optimisation of volume only (do not modify rprim, and allow an homogeneous dilatation of the three components of acell) optcell=2 : full optimization of cell geometry (modify acell and rprim - normalize the vectors of rprim to generate the acell). This is the usual mode for cell shape and volume optimization. It takes into account the symmetry of the system, so that only the effectively relevant degrees of freedom are optimized. optcell=3 : constant-volume optimization of cell geometry (modify acell and rprim under constraint - normalize the vectors of rprim to generate the acell) optcell=4,5 or 6 : optimize acell(1), acell(2) or acell(3), respectively (only works if the two other vectors are orthogonal to the optimized one, the latter being along its cartesian axis). optcell=7,8 or 9 : optimize the cell geometry while keeping the first, second or third vector unchanged (only works if the two other vectors are orthogonal to the one left unchanged, the latter being along its cartesian axis). **strtarget 目標圧力。単位は(Ha/Bohr^3)。セルを最適化する際に必要。 1(Ha/Bohr^3)=29421.033GPa。 テンソル表記もできる。 2010-04-03T03:03:28+09:00 1270231408 https://w.atwiki.jp/abinit/pages/14.html *変数(Variables) [[VARBAS]]　基本変数 [[VARDEV]] [[VARFIL]] [[VARGEO]] ジオメトリー・対象性に関する変数 [[VARGS]] 基底状態計算変数 [[VARGW]] [[VARINT]] [[VARPAR]] [[VARPAW]] [[VARRF]] [[VARRLX]]　構造最適化・構造緩和の変数 [[VARW90]] 2010-04-03T02:37:48+09:00 1270229868 https://w.atwiki.jp/abinit/pages/2.html **メニュー -[[トップページ]] -[[変数]] -[[チュートリアル]] ---- **リンク -[[abinit>http://www.abinit.org/]] -[[管理人HP>http://remiliahxahxa.iza-yoi.net/]] -[[@wiki>>http://atwiki.jp]] &link_editmenu(text=ここを編集) 2010-04-02T23:50:20+09:00 1270219820 https://w.atwiki.jp/abinit/pages/13.html *管理人の意図 私は某所で大学院生をしているものです。 専門は物質科学（大きく分野を広げているのは人物の特定を避けるためです）で 古典のMD、そしてabinitをいじったりしています。 実験もやります。 このwikiの意図は主に個人メモ的なものが主であり私が重要と思う変数とかその他いろいろなことをメモしていきたいと思っています。 つまりいちいちabinitのホームページを見ないでも（何故か重い）作業できる早見表を作りたい程度の意図です。 2010-04-02T23:46:45+09:00 1270219605 https://w.atwiki.jp/abinit/pages/1.html abinit@wikiへようこそ -ABINITとは、VASPと同様に固体結晶の電子状態を密度汎関数で計算するプログラムパッケージです。 -フリーソフトです -本家はココです[[abinit.org>http://www.abinit.org/]] -[[管理人の意図]] **バグ・不具合を見つけたら？ 要望がある場合は？ お手数ですが、メールでお問い合わせください。 covenant-dominate(あっとまーくだよ☆ミ)hotmail.co.jp 2010-04-02T23:41:58+09:00 1270219318 https://w.atwiki.jp/abinit/pages/8.html * 動画(youtube) @wikiのwikiモードでは #video(動画のURL) と入力することで、動画を貼り付けることが出来ます。 詳しくはこちらをご覧ください。 ＝＞http://atwiki.jp/guide/17_209_ja.html また動画のURLはYoutubeのURLをご利用ください。 ＝＞http://www.youtube.com/ ----- たとえば、#video(http://youtube.com/watch?v=kTV1CcS53JQ)と入力すると以下のように表示されます。 #video(http://youtube.com/watch?v=kTV1CcS53JQ) 2010-04-02T23:32:52+09:00 1270218772