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abimkdocs/variables_abinit.py
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@ -547,7 +547,7 @@ Other related input variables are:
* in case of [[berryopt]]=1,2, or 3: [[bdberry]] and [[kberry]]; also, [[nberry]] must be larger than 0;
* in case of [[berryopt]]=-1,-2, or -3: the variable [[rfdir]] must be used to specify the primitive vector along which the projection of the polarization or the ddk will be computed. For example if [[berryopt]]=-1 and [[rfdir]]=1 0 0, the projection of the polarization along the reciprocal lattice vector G_1 is computed. In case [[rfdir]]=1 1 1, ABINIT computes the projection of P along G_1, G_2 and G_3 and transforms the results to cartesian coordinates;
* in cases where [[berryopt]] is negative, [[berrystep]] allow a computation of multiple-step Berry phase in order to accelerate the convergence.
* [[efield]] and [[rfdir]] in case of [[berryopt]]=4 ;
* [[efield]] and [[rfdir]] in case of [[berryopt]]=4;
The cases [[berryopt]]=-1,-2,-3, 4, 6, 7, 14, 16, and 17 have to be used with [[occopt]]=1.
@ -1482,7 +1482,7 @@ correlation grid.
When [[chksymbreak]]=1, the code stops (or issue a warning) if:
* (1) The k point grid is non-symmetric, in case [[kptopt]] =1, 2, or 4 ;
* (1) The k point grid is non-symmetric, in case [[kptopt]] =1, 2, or 4;
* (2) The non-symmorphic translation part of the symmetry operations has components that are not zero,
or simple fractions, with 2, 3, 4, 6, 8 or 12 as denominators.
@ -6562,8 +6562,8 @@ The possible values of [[iprcel]] correspond to:
* Between 41 and 49 --> compute the RPA dielectric matrix at the first step, and recompute it at a later step, and take into account the mixing factor [[diemix]].
* Between 51 and 59 --> same as between 41 and 49, but compute the RPA dielectric matrix by another mean
* Between 61 and 69 --> same as between 41 and 49, but compute the electronic dielectric matrix instead of the RPA one.
* Between 71 and 78 --> STILL UNDER DEVELOPMENT -- NOT USABLE ; Use the modified Kerker preconditioner with a real-space formulation (basic formulation is shown at [[dielng]]). The dielectric matrix is approximated thanks to [[diemac]] and [[dielng]]. Note that [[diemix]] is also used.
* 79 --> STILL UNDER DEVELOPMENT -- NOT USABLE ; same as previous but with an alternate algorithm.
* Between 71 and 78 --> STILL UNDER DEVELOPMENT -- NOT USABLE; Use the modified Kerker preconditioner with a real-space formulation (basic formulation is shown at [[dielng]]). The dielectric matrix is approximated thanks to [[diemac]] and [[dielng]]. Note that [[diemix]] is also used.
* 79 --> STILL UNDER DEVELOPMENT -- NOT USABLE; same as previous but with an alternate algorithm.
* 141 to 169 --> same as Between 41 and 69 (but, the dielectric matrix is also recomputed every iprcel modulo 10 step).
The computation of the dielectric matrix (for 0 [100]< [[iprcel]] < 70 [100])
@ -7317,7 +7317,7 @@ The value [[ixc]]=10 is used internally: gives the difference between
* 18 --> (NOT AVAILABLE: used internally for GGA BLYP pseudopotentials from M. Krack, see Theor. Chem. Acc. 114, 145 (2005), available from the [ CP2K repository ](https://github.com/cp2k/cp2k/tree/master/potentials/Goedecker/abinit/blyp) \- use the LibXC instead, with [[ixc]]=-106131.
* 19 --> (NOT AVAILABLE: used internally for GGA BP86 pseudopotentials from M. Krack, see Theor. Chem. Acc. 114, 145 (2005), available from the [ CP2K repository ](https://github.com/cp2k/cp2k/tree/master/potentials/Goedecker/abinit/bp) \- use the LibXC instead, with [[ixc]]=-106132.
* 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.
* 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).
@ -7363,10 +7363,10 @@ This means having [[usekden]]=1.
* 008 --> XC_LDA_C_VWN_RPA ! Vosko, Wilk, & Nussair (RPA) [SH Vosko, L Wilk, and M Nusair, Can. J. Phys. 58, 1200 (1980) ]
* 009 --> XC_LDA_C_PZ ! Perdew & Zunger [[cite:Perdew1981]]
* 010 --> XC_LDA_C_PZ_MOD ! Perdew & Zunger (Modified) [[cite:Perdew1981]] Modified to improve the matching between the low and high rs part ]
* 011 --> XC_LDA_C_OB_PZ ! Ortiz & Ballone (PZ) [G Ortiz and P Ballone, Phys. Rev. B 50, 1391 (1994) ; G Ortiz and P Ballone, Phys. Rev. B 56, 9970(E) (1997) ; [[cite:Perdew1981]] ]
* 011 --> XC_LDA_C_OB_PZ ! Ortiz & Ballone (PZ) [G Ortiz and P Ballone, Phys. Rev. B 50, 1391 (1994); G Ortiz and P Ballone, Phys. Rev. B 56, 9970(E) (1997); [[cite:Perdew1981]] ]
* 012 --> XC_LDA_C_PW ! Perdew & Wang [JP Perdew and Y Wang, Phys. Rev. B 45, 13244 (1992) ]
* 013 --> XC_LDA_C_PW_MOD ! Perdew & Wang (Modified) [JP Perdew and Y Wang, Phys. Rev. B 45, 13244 (1992) ; Added extra digits to some constants as in the PBE routine see [ https://www.chem.uci.edu/~kieron/dftold2/pbe.php ](https://www.chem.uci.edu/~kieron/dftold2/pbe.php) (at some point it was available at http://dft.uci.edu/pbe.php) ]
* 014 --> XC_LDA_C_OB_PW ! Ortiz & Ballone (PW) [G Ortiz and P Ballone, Phys. Rev. B 50, 1391 (1994) ; G Ortiz and P Ballone, Phys. Rev. B 56, 9970(E) (1997) ; JP Perdew and Y Wang, Phys. Rev. B 45, 13244 (1992) ]
* 013 --> XC_LDA_C_PW_MOD ! Perdew & Wang (Modified) [JP Perdew and Y Wang, Phys. Rev. B 45, 13244 (1992); Added extra digits to some constants as in the PBE routine see [ https://www.chem.uci.edu/~kieron/dftold2/pbe.php ](https://www.chem.uci.edu/~kieron/dftold2/pbe.php) (at some point it was available at http://dft.uci.edu/pbe.php) ]
* 014 --> XC_LDA_C_OB_PW ! Ortiz & Ballone (PW) [G Ortiz and P Ballone, Phys. Rev. B 50, 1391 (1994); G Ortiz and P Ballone, Phys. Rev. B 56, 9970(E) (1997); JP Perdew and Y Wang, Phys. Rev. B 45, 13244 (1992) ]
* 017 --> XC_LDA_C_vBH ! von Barth & Hedin [U von Barth and L Hedin, J. Phys. C: Solid State Phys. 5, 1629 (1972) ]
* 020 --> XC_LDA_XC_TETER93 ! Teter 93 parametrization [S Goedecker, M Teter, J Hutter, PRB 54, 1703 (1996) ]
* 022 --> XC_LDA_C_ML1 ! Modified LSD (version 1) of Proynov and Salahub [EI Proynov and D Salahub, Phys. Rev. B 49, 7874 (1994) ]
@ -7385,7 +7385,7 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
* 85 --> XC_GGA_C_OP_G96 ! one-parameter progressive functional (G96 version) [T Tsuneda, T Suzumura, and K Hirao, J. Chem. Phys. 111, 5656 (1999) ]
* 86 --> XC_GGA_C_OP_PBE ! one-parameter progressive functional (PBE version) [T Tsuneda, T Suzumura, and K Hirao, J. Chem. Phys. 111, 5656 (1999) ]
* 87 --> XC_GGA_C_OP_B88 ! one-parameter progressive functional (B88 version) [T Tsuneda, T Suzumura, and K Hirao, J. Chem. Phys. 111, 5656 (1999) ]
* 88 --> XC_GGA_C_FT97 ! Filatov & Thiel correlation [M Filatov & W Thiel, Int. J. Quant. Chem. 62, 603-616 (1997) ; M Filatov & W Thiel, Mol Phys 91, 847 (1997) ] WARNING: this functional is not tested. Use at your own risks.
* 88 --> XC_GGA_C_FT97 ! Filatov & Thiel correlation [M Filatov & W Thiel, Int. J. Quant. Chem. 62, 603-616 (1997); M Filatov & W Thiel, Mol Phys 91, 847 (1997) ] WARNING: this functional is not tested. Use at your own risks.
* 89 --> XC_GGA_C_SPBE ! PBE correlation to be used with the SSB exchange [M Swart, M Sola, and FM Bickelhaupt, J. Chem. Phys. 131, 094103 (2009) ]
* 90 --> XC_GGA_X_SSB_SW ! Swarta, Sola and Bickelhaupt correction to PBE [M Swart, M Sola, and FM Bickelhaupt, J. Comp. Meth. Sci. Engin. 9, 69 (2009) ]
* 91 --> XC_GGA_X_SSB ! WARNING: This functional gives NaN on IBM (XG20130608). Swarta, Sola and Bickelhaupt [M Swart, M Sola, and FM Bickelhaupt, J. Chem. Phys. 131, 094103 (2009) ]
@ -7398,15 +7398,15 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
* 98 --> XC_GGA_X_BPCCAC ! BPCCAC (GRAC for the energy) [E Bremond, D Pilard, I Ciofini, H Chermette, C Adamo, and P Cortona, Theor Chem Acc 131, 1184 (2012) ]
* 99 --> XC_GGA_C_REVTCA ! Tognetti, Cortona, Adamo (revised) [V Tognetti, P Cortona, and C Adamo, Chem. Phys. Lett. 460, 536-539 (2008) ]
* 100 --> XC_GGA_C_TCA ! Tognetti, Cortona, Adamo [V Tognetti, P Cortona, and C Adamo, J. Chem. Phys. 128, 034101 (2008) ]
* 101 --> XC_GGA_X_PBE ! Perdew, Burke & Ernzerhof exchange [JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996) ; JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 78, 1396(E) (1997) ]
* 101 --> XC_GGA_X_PBE ! Perdew, Burke & Ernzerhof exchange [JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996); JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 78, 1396(E) (1997) ]
* 102 --> XC_GGA_X_PBE_R ! Perdew, Burke & Ernzerhof exchange (revised) [Y Zhang and W Yang, Phys. Rev. Lett 80, 890 (1998) ]
* 103 --> XC_GGA_X_B86 ! Becke 86 Xalfa,beta,gamma [AD Becke, J. Chem. Phys 84, 4524 (1986) ]
* 104 --> XC_GGA_X_HERMAN ! Herman Xalphabeta GGA [F Herman, JP Van Dyke, and IB Ortenburger, Phys. Rev. Lett. 22, 807 (1969) ; F Herman, IB Ortenburger, and JP Van Dyke, Int. J. Quantum Chem. Symp. 3, 827 (1970) ]
* 105 --> XC_GGA_X_B86_MGC ! Becke 86 Xalfa,beta,gamma (with mod. grad. correction) [AD Becke, J. Chem. Phys 84, 4524 (1986) ; AD Becke, J. Chem. Phys 85, 7184 (1986) ]
* 104 --> XC_GGA_X_HERMAN ! Herman Xalphabeta GGA [F Herman, JP Van Dyke, and IB Ortenburger, Phys. Rev. Lett. 22, 807 (1969); F Herman, IB Ortenburger, and JP Van Dyke, Int. J. Quantum Chem. Symp. 3, 827 (1970) ]
* 105 --> XC_GGA_X_B86_MGC ! Becke 86 Xalfa,beta,gamma (with mod. grad. correction) [AD Becke, J. Chem. Phys 84, 4524 (1986); AD Becke, J. Chem. Phys 85, 7184 (1986) ]
* 106 --> XC_GGA_X_B88 ! Becke 88 [AD Becke, Phys. Rev. A 38, 3098 (1988) ]
* 107 --> XC_GGA_X_G96 ! Gill 96 [PMW Gill, Mol. Phys. 89, 433 (1996) ]
* 108 --> XC_GGA_X_PW86 ! Perdew & Wang 86 [JP Perdew and Y Wang, Phys. Rev. B 33, 8800 (1986) ]
* 109 --> XC_GGA_X_PW91 ! Perdew & Wang 91 [JP Perdew, in Proceedings of the 21st Annual International Symposium on the Electronic Structure of Solids, ed. by P Ziesche and H Eschrig (Akademie Verlag, Berlin, 1991), p. 11. ; JP Perdew, JA Chevary, SH Vosko, KA Jackson, MR Pederson, DJ Singh, and C Fiolhais, Phys. Rev. B 46, 6671 (1992) ; JP Perdew, JA Chevary, SH Vosko, KA Jackson, MR Pederson, DJ Singh, and C Fiolhais, Phys. Rev. B 48, 4978(E) (1993) ]
* 109 --> XC_GGA_X_PW91 ! Perdew & Wang 91 [JP Perdew, in Proceedings of the 21st Annual International Symposium on the Electronic Structure of Solids, ed. by P Ziesche and H Eschrig (Akademie Verlag, Berlin, 1991), p. 11.; JP Perdew, JA Chevary, SH Vosko, KA Jackson, MR Pederson, DJ Singh, and C Fiolhais, Phys. Rev. B 46, 6671 (1992); JP Perdew, JA Chevary, SH Vosko, KA Jackson, MR Pederson, DJ Singh, and C Fiolhais, Phys. Rev. B 48, 4978(E) (1993) ]
* 110 --> XC_GGA_X_OPTX ! Handy & Cohen OPTX 01 [NC Handy and AJ Cohen, Mol. Phys. 99, 403 (2001) ]
* 111 --> XC_GGA_X_DK87_R1 ! dePristo & Kress 87 (version R1) [AE DePristo and JD Kress, J. Chem. Phys. 86, 1425 (1987) ]
* 112 --> XC_GGA_X_DK87_R2 ! dePristo & Kress 87 (version R2) [AE DePristo and JD Kress, J. Chem. Phys. 86, 1425 (1987) ]
@ -7417,18 +7417,18 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
* 117 --> XC_GGA_X_RPBE ! Hammer, Hansen & Norskov (PBE-like) [B Hammer, LB Hansen and JK Norskov, Phys. Rev. B 59, 7413 (1999) ]
* 118 --> XC_GGA_X_WC ! Wu & Cohen [Z Wu and RE Cohen, Phys. Rev. B 73, 235116 (2006) ]
* 119 --> XC_GGA_X_mPW91 ! Modified form of PW91 by Adamo & Barone [C Adamo and V Barone, J. Chem. Phys. 108, 664 (1998) ]
* 120 --> XC_GGA_X_AM05 ! Armiento & Mattsson 05 exchange [R Armiento and AE Mattsson, Phys. Rev. B 72, 085108 (2005) ; AE Mattsson, R Armiento, J Paier, G Kresse, JM Wills, and TR Mattsson, J. Chem. Phys. 128, 084714 (2008) ]
* 120 --> XC_GGA_X_AM05 ! Armiento & Mattsson 05 exchange [R Armiento and AE Mattsson, Phys. Rev. B 72, 085108 (2005); AE Mattsson, R Armiento, J Paier, G Kresse, JM Wills, and TR Mattsson, J. Chem. Phys. 128, 084714 (2008) ]
* 121 --> XC_GGA_X_PBEA ! Madsen (PBE-like) [G Madsen, Phys. Rev. B 75, 195108 (2007) ]
* 122 --> XC_GGA_X_MPBE ! Adamo & Barone modification to PBE [C Adamo and V Barone, J. Chem. Phys. 116, 5933 (2002) ]
* 123 --> XC_GGA_X_XPBE ! xPBE reparametrization by Xu & Goddard [X Xu and WA Goddard III, J. Chem. Phys. 121, 4068 (2004) ]
* 125 --> XC_GGA_X_BAYESIAN ! Bayesian best fit for the enhancement factor [JJ Mortensen, K Kaasbjerg, SL Frederiksen, JK Norskov, JP Sethna, and KW Jacobsen, Phys. Rev. Lett. 95, 216401 (2005) ]
* 126 --> XC_GGA_X_PBE_JSJR ! PBE JSJR reparametrization by Pedroza, Silva & Capelle [LS Pedroza, AJR da Silva, and K. Capelle, Phys. Rev. B 79, 201106(R) (2009) ]
* 130 --> XC_GGA_C_PBE ! Perdew, Burke & Ernzerhof correlation [JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996) ; JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 78, 1396(E) (1997) ]
* 130 --> XC_GGA_C_PBE ! Perdew, Burke & Ernzerhof correlation [JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996); JP Perdew, K Burke, and M Ernzerhof, Phys. Rev. Lett. 78, 1396(E) (1997) ]
* 131 --> XC_GGA_C_LYP ! Lee, Yang & Parr [C Lee, W Yang and RG Parr, Phys. Rev. B 37, 785 (1988) B Miehlich, A Savin, H Stoll and H Preuss, Chem. Phys. Lett. 157, 200 (1989) ]
* 132 --> XC_GGA_C_P86 ! Perdew 86 [JP Perdew, Phys. Rev. B 33, 8822 (1986) ]
* 133 --> XC_GGA_C_PBE_SOL ! Perdew, Burke & Ernzerhof correlation SOL [JP Perdew, et al, Phys. Rev. Lett. 100, 136406 (2008) ]
* 134 --> XC_GGA_C_PW91 ! Perdew & Wang 91 [JP Perdew, JA Chevary, SH Vosko, KA Jackson, MR Pederson, DJ Singh, and C Fiolhais, Phys. Rev. B 46, 6671 (1992) ]
* 135 --> XC_GGA_C_AM05 ! Armiento & Mattsson 05 correlation [ R Armiento and AE Mattsson, Phys. Rev. B 72, 085108 (2005) ; AE Mattsson, R Armiento, J Paier, G Kresse, JM Wills, and TR Mattsson, J. Chem. Phys. 128, 084714 (2008) ]
* 135 --> XC_GGA_C_AM05 ! Armiento & Mattsson 05 correlation [ R Armiento and AE Mattsson, Phys. Rev. B 72, 085108 (2005); AE Mattsson, R Armiento, J Paier, G Kresse, JM Wills, and TR Mattsson, J. Chem. Phys. 128, 084714 (2008) ]
* 136 --> XC_GGA_C_XPBE ! xPBE reparametrization by Xu & Goddard [X Xu and WA Goddard III, J. Chem. Phys. 121, 4068 (2004) ]
* 137 --> XC_GGA_C_LM ! Langreth and Mehl correlation [DC Langreth and MJ Mehl, Phys. Rev. Lett. 47, 446 (1981) ]
* 138 --> XC_GGA_C_PBE_JRGX ! JRGX reparametrization by Pedroza, Silva & Capelle [LS Pedroza, AJR da Silva, and K. Capelle, Phys. Rev. B 79, 201106(R) (2009) ]
@ -7443,7 +7443,7 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
* 147 --> XC_GGA_C_WL ! Wilson & Levy [LC Wilson and M Levy, Phys. Rev. B 41, 12930 (1990) ]
* 148 --> XC_GGA_C_WI ! Wilson & Ivanov [LC Wilson & S Ivanov, Int. J. Quantum Chem. 69, 523-532 (1998) ]
* 149 --> XC_GGA_X_MB88 ! Modified Becke 88 for proton transfer [V Tognetti and C Adamo, J. Phys. Chem. A 113, 14415-14419 (2009) ]
* 150 --> XC_GGA_X_SOGGA ! Second-order generalized gradient approximation [Y Zhao and DG Truhlar, J. Chem. Phys. 128, 184109 (2008) ; http://comp.chem.umn.edu/mfm/index.html ]
* 150 --> XC_GGA_X_SOGGA ! Second-order generalized gradient approximation [Y Zhao and DG Truhlar, J. Chem. Phys. 128, 184109 (2008); http://comp.chem.umn.edu/mfm/index.html ]
* 151 --> XC_GGA_X_SOGGA11 ! Second-order generalized gradient approximation 2011 [R Peverati, Y Zhao, and DG Truhlar, J. Phys. Chem. Lett. 2, 1911-1997 (2011); http://comp.chem.umn.edu/mfm/index.html ]
* 152 --> XC_GGA_C_SOGGA11 ! Second-order generalized gradient approximation 2011 [R Peverati, Y Zhao, and DG Truhlar, J. Phys. Chem. Lett. 2, 1911-1997 (2011); http://comp.chem.umn.edu/mfm/index.html ]
* 153 --> XC_GGA_C_WI0 ! Wilson & Ivanov initial version [LC Wilson & S Ivanov, Int. J. Quantum Chem. 69, 523-532 (1998) ]
@ -7474,7 +7474,7 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
* 179 --> XC_GGA_XC_SB98_2a ! Schmider-Becke 98 parameterization 2a [HL Schmider and AD Becke, J. Chem. Phys. 108, 9624 (1998) ]
* 180 --> XC_GGA_XC_SB98_2b ! Schmider-Becke 98 parameterization 2b [HL Schmider and AD Becke, J. Chem. Phys. 108, 9624 (1998) ]
* 181 --> XC_GGA_XC_SB98_2c ! Schmider-Becke 98 parameterization 2c [HL Schmider and AD Becke, J. Chem. Phys. 108, 9624 (1998) ]
* 183 --> XC_GGA_X_OL2 ! Exchange form based on Ou-Yang and Levy v.2 [P Fuentealba and O Reyes, Chem. Phys. Lett. 232, 31-34 (1995) ; H Ou-Yang, M Levy, Int. J. of Quant. Chem. 40, 379-388 (1991) ]
* 183 --> XC_GGA_X_OL2 ! Exchange form based on Ou-Yang and Levy v.2 [P Fuentealba and O Reyes, Chem. Phys. Lett. 232, 31-34 (1995); H Ou-Yang, M Levy, Int. J. of Quant. Chem. 40, 379-388 (1991) ]
* 184 --> XC_GGA_X_APBE ! mu fixed from the semiclassical neutral atom [LA Constantin, E Fabiano, S Laricchia, and F Della Sala, Phys. Rev. Lett. 106, 186406 (2011) ]
* 186 --> XC_GGA_C_APBE ! mu fixed from the semiclassical neutral atom [LA Constantin, E Fabiano, S Laricchia, and F Della Sala, Phys. Rev. Lett. 106, 186406 (2011) ]
* 191 --> XC_GGA_X_HTBS! Haas, Tran, Blaha, and Schwarz [P Haas, F Tran, P Blaha, and K Schwarz, Phys. Rev. B 83, 205117 (2011) ]
@ -7497,7 +7497,7 @@ GGA functionals (do not forget to add a minus sign, as discussed above)
MetaGGA functionals (do not forget to add a minus sign, as discussed above).
See Sun et al, PRB 84, 035117 (2011) for the formulas.
* 202 --> XC_MGGA_X_TPSS ! Tao, Perdew, Staroverov & Scuseria [J Tao, JP Perdew, VN Staroverov, and G Scuseria, Phys. Rev. Lett. 91, 146401 (2003) ; JP Perdew, J Tao, VN Staroverov, and G Scuseria, J. Chem. Phys. 120, 6898 (2004) ]
* 202 --> XC_MGGA_X_TPSS ! Tao, Perdew, Staroverov & Scuseria [J Tao, JP Perdew, VN Staroverov, and G Scuseria, Phys. Rev. Lett. 91, 146401 (2003); JP Perdew, J Tao, VN Staroverov, and G Scuseria, J. Chem. Phys. 120, 6898 (2004) ]
* 203 --> XC_MGGA_X_M06L ! Zhao, Truhlar exchange [Y Zhao and DG Truhlar, JCP 125, 194101 (2006); Y Zhao and DG Truhlar, Theor. Chem. Account 120, 215 (2008) ]
* 204 --> XC_MGGA_X_GVT4 ! GVT4 (X part of VSXC) from van Voorhis and Scuseria [T Van Voorhis and GE Scuseria, JCP 109, 400 (1998) ]
* 205 --> XC_MGGA_X_TAU_HCTH ! tau-HCTH from Boese and Handy [AD Boese and NC Handy, JCP 116, 9559 (2002) ]
@ -7828,7 +7828,7 @@ lattice, the conversion might be more difficult. See the description of
cartesian coordinates to the primitive vectors in the reciprocal space. In
order to help a bit, we list below a series of typical values, for the FCC,
BCC, hexagonal and rhombohedral Bravais lattices. Note: all the data below
are given in dimensionless units ; they have to be rescaled by the actual
are given in dimensionless units; they have to be rescaled by the actual
lengths defined by the [[acell]] values. However, [[kptbounds]] values can be
used as such, if the values of [[rprim]] given below are adopted.
@ -7871,9 +7871,9 @@ the work: L-Gamma-X-W-K,U-L-W-X-K,U-Gamma with
The lengths of segments (this information is useful to draw the band
structure, with the correct relative scale between special points) can be
found using the conventional cartesian coordinates:
l(L-Gamma)=sqrt(3)/4=0.433... ; l(Gamma-X)=1/2=0.5 ; l(X-W)=1/4=0.25 ;
l(W-K)=sqrt(2)/8=0.177... ; l(K-L)=sqrt(6)/8=0.306... ;
l(L-W)=sqrt(2)/4=0.354... ; l(W-X)=1/4=0.25 ; l(X-K)=sqrt(2)/8=0.177... ;
l(L-Gamma)=sqrt(3)/4=0.433...; l(Gamma-X)=1/2=0.5; l(X-W)=1/4=0.25;
l(W-K)=sqrt(2)/8=0.177...; l(K-L)=sqrt(6)/8=0.306...;
l(L-W)=sqrt(2)/4=0.354...; l(W-X)=1/4=0.25; l(X-K)=sqrt(2)/8=0.177...;
l(K-Gamma)=sqrt(2).3/8=0.530...
B. **BCC lattice**
@ -7897,9 +7897,9 @@ So, if you want to specify a typical circuit, the following might do the work: G
The lengths of segments (this information is useful to draw the band
structure, with the correct relative scale between special points) can be
found using the conventional cartesian coordinates: l(Gamma-H)=1/2=0.5 ;
l(H-N)=sqrt(2)/4=0.354... ; l(N-Gamma)=sqrt(2)/4=0.354... ;
l(Gamma-P)=sqrt(3)/4=0.433... ; l(P-N)=1/4=0.25 ; l(N-P)=1/4=0.25 ;
found using the conventional cartesian coordinates: l(Gamma-H)=1/2=0.5;
l(H-N)=sqrt(2)/4=0.354...; l(N-Gamma)=sqrt(2)/4=0.354...;
l(Gamma-P)=sqrt(3)/4=0.433...; l(P-N)=1/4=0.25; l(N-P)=1/4=0.25;
l(P-H)=sqrt(3)/4=0.433...
C. **Hexagonal lattices**
@ -7928,12 +7928,12 @@ one needs to know the a and c lattice parameters. Also, in what follows, we
omit the 2*pi factor sometimes present in the definition of the reciprocal
space vectors. The reciprocal vectors are (1/a 1/(sqrt(3)*a) 0), (0
2/(sqrt(3)*a) 0), (0 0 1/c). The lengths of the above-mentioned segments can
be computed as: l(K-Gamma)=2/(3*a)=0.666.../a ;
l(Gamma-M)=1/(sqrt(3)*a)=0.577.../a ; l(M-K)=1/(3*a)=0.333.../a ;
l(K-H)=1/(2*c)=0.5.../c ; l(H-A)=2/(3*a)=0.666.../a ;
l(A-L)=1/(sqrt(3)*a)=0.577.../a ; l(L-H)=1/(3*a)=0.333.../a ;
l(H-L)=1/(3*a)=0.333.../a ; l(L-M)=1/(2*c)=0.5.../c ;
l(M-Gamma)=-1/(sqrt(3)*a)=0.577.../a ; l(Gamma-A)=1/(2*c)=0.5.../c
be computed as: l(K-Gamma)=2/(3*a)=0.666.../a;
l(Gamma-M)=1/(sqrt(3)*a)=0.577.../a; l(M-K)=1/(3*a)=0.333.../a;
l(K-H)=1/(2*c)=0.5.../c; l(H-A)=2/(3*a)=0.666.../a;
l(A-L)=1/(sqrt(3)*a)=0.577.../a; l(L-H)=1/(3*a)=0.333.../a;
l(H-L)=1/(3*a)=0.333.../a; l(L-M)=1/(2*c)=0.5.../c;
l(M-Gamma)=-1/(sqrt(3)*a)=0.577.../a; l(Gamma-A)=1/(2*c)=0.5.../c
D. **Rhombohedral lattices**
@ -7984,7 +7984,7 @@ space vectors. The reciprocal vectors are (2/(3*a) 0 1/(3*c)), -(1/(3*a)
1/(sqrt(3)*a) 1/(3*c), -(1/(3*a) -1/(sqrt(3)*a) 1/(3*c) ). The lengths of the
above-mentioned segments can be computed as:
l(X-Gamma)=2/(sqrt(3)*a)=1.155.../a, with
l(K-Gamma)=(1+(a/c)^2/4)*4/(3*sqrt(3)*a); l(Gamma-T)=1/(2*c) ;
l(K-Gamma)=(1+(a/c)^2/4)*4/(3*sqrt(3)*a); l(Gamma-T)=1/(2*c);
l(T-L)=2/(sqrt(3)*a)=1.155.../a, with l(T-W)=(1-(a/c)^2/2)*4/(3*sqrt(3)*a);
l(L-Gamma)=sqrt(4/(a^2)+1/(c^2))/3 l(Gamma-X)=sqrt(1/(a^2)+1/(c^2))*2/3
""",
@ -8599,17 +8599,17 @@ Compatible with all MEP search methods.
Compatible only with Nudged Elastic Band ([[imgmov]]=5).
_See, for instance: J. Chem. Phys. 128, 134106 (2008)._
* 2 --> **Local Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm** ; each image along the band is minimized with a different instance of the BFGS optimizer.
* 2 --> **Local Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm**; each image along the band is minimized with a different instance of the BFGS optimizer.
Compatible only with Nudged Elastic Band ([[imgmov]]=5).
_See, for instance: J. Chem. Phys. 128, 134106 (2008)._
IN [[DEVELOP]]PMENT - NOT RELIABLE
* 3 --> **Global Broyden-Fletcher-Goldfarb-Shanno (GL-BFGS) algorithm** ; all images along the band are minimized with a single instance of the BFGS optimizer.
* 3 --> **Global Broyden-Fletcher-Goldfarb-Shanno (GL-BFGS) algorithm**; all images along the band are minimized with a single instance of the BFGS optimizer.
Compatible only with Nudged Elastic Band ([[imgmov]]=5).
_See, for instance: J. Chem. Phys. 128, 134106 (2008)._
IN [[DEVELOP]]PMENT - NOT RELIABLE
* 4 --> **Fourth-order Runge-Kutta method** ; the images along the band are moved every four steps (1 <=istep<=[[ntimimage]]) following the Runge-Kutta algorithm, the time step being [[fxcartfactor]].
* 4 --> **Fourth-order Runge-Kutta method**; the images along the band are moved every four steps (1 <=istep<=[[ntimimage]]) following the Runge-Kutta algorithm, the time step being [[fxcartfactor]].
Compatible only with Simplified String Method ([[imgmov]]=2 and
[[string_algo]]=1 or 2).
_See: J. Chem. Phys. 126, 164103 (2007)._
@ -9063,7 +9063,7 @@ Variable(
[[nbdbuf]] gives the number of bands, the highest in energy, that, among the
[[nband]] bands, are to be considered as part of a buffer. This concept is
useful in three situations: in non-self-consistent calculations, for the
determination of the convergence tolerance ; for response functions of metals,
determination of the convergence tolerance; for response functions of metals,
to avoid instabilities, and also when finite electric fields or non-linear
responses (with electric field perturbations) are considered. For the two
first, the need of a buffer is a natural requirement of the problem, so that
@ -9189,28 +9189,28 @@ file:
netcdf md32.outH_moldyn1 {
dimensions:
time = UNLIMITED ; // (11 currently)
DimTensor = 6 ;
DimCoord = 3 ;
NbAtoms = 32 ;
DimVector = 3 ;
DimScalar = 1 ;
time = UNLIMITED; // (11 currently)
DimTensor = 6;
DimCoord = 3;
NbAtoms = 32;
DimVector = 3;
DimScalar = 1;
variables:
double E_pot(time) ;
E_pot:units = "hartree" ;
double E_kin(time) ;
E_kin:units = "hartree" ;
double Stress(time, DimTensor) ;
Stress:units = "hartree/Bohr^3" ;
double Position(time, DimCoord, NbAtoms) ;
Position:units = "Bohr" ;
double Celerity(time, DimCoord, NbAtoms) ;
Celerity:units = "Bohr/(atomic time unit)" ;
double PrimitiveVector1(DimVector) ;
double PrimitiveVector2(DimVector) ;
double PrimitiveVector3(DimVector) ;
double Cell_Volume(DimScalar) ;
Cell_Volume:units = "Bohr^3" ;
double E_pot(time);
E_pot:units = "hartree";
double E_kin(time);
E_kin:units = "hartree";
double Stress(time, DimTensor);
Stress:units = "hartree/Bohr^3";
double Position(time, DimCoord, NbAtoms);
Position:units = "Bohr";
double Celerity(time, DimCoord, NbAtoms);
Celerity:units = "Bohr/(atomic time unit)";
double PrimitiveVector1(DimVector);
double PrimitiveVector2(DimVector);
double PrimitiveVector3(DimVector);
double Cell_Volume(DimScalar);
Cell_Volume:units = "Bohr^3";
}
""",
),
@ -10505,7 +10505,7 @@ allowed x, y and z magnetization (useful only with [[nspinor]]=2 and
symmetry - and thus spontaneous magnetization, or with spin-orbit, if one
allows for spontaneous non-collinear magnetism). Not yet available for
response functions. Also note that, with [[nspden]]=4, time-reversal symmetry
is not taken into account (at present ; this has to be checked) and thus
is not taken into account (at present; this has to be checked) and thus
[[kptopt]] has to be different from 1 or 2.
The default ([[nspden]]=[[nsppol]]) does not suit the case of vector magnetization.
@ -11796,7 +11796,7 @@ If set to 0, all lm-moments of the sphere contributions to the density are
computed at each electronic iteration.
If set to 1, only non-zero lm-moments of the sphere contributions to the
density are computed at each electronic iteration (they are all computed at
the first iteration then only those found to be non-zero will be computed ;
the first iteration then only those found to be non-zero will be computed;
thus the first iteration is more cpu intensive)
""",
),
@ -14641,7 +14641,7 @@ Variable(
characteristics=['[[DEVELOP]]'],
text="""
Used in Recursion method ([[tfkinfunc]]=2). Determine the number of
discretisation points to compute some path integral in the recursion method ;
discretisation points to compute some path integral in the recursion method;
those path integrals are used to compute the entropy and the eigenvalues
energy. during the latest SFC cycles.
""",
@ -14984,7 +14984,7 @@ with respect to k, independently of the electric field perturbation itself.
electric field are different, one often does the calculation of derivatives in
a separate dataset, followed by calculation of electric field response as well
as phonon.
The options 2 and 3 proves useful in that context ; also, in case a scissor
The options 2 and 3 proves useful in that context; also, in case a scissor
shift is to be used, it is usually not applied for the d/dk response).
""",
),
@ -15910,8 +15910,8 @@ Variable(
defaultval=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
mnemonics="STRess TARGET",
text="""
The components of the stress tensor must be stored according to: (1,1)->1 ;
(2,2)->2 ; (3,3)->3 ; (2,3)->4 ; (3,1)->5 ; (1,2)->6\. The conversion factor
The components of the stress tensor must be stored according to: (1,1)->1;
(2,2)->2; (3,3)->3; (2,3)->4; (3,1)->5; (1,2)->6\. The conversion factor
between Ha/Bohr**3 and GPa is: 1 Ha/Bohr**3 = 29421.033d0 GPa.
Not used if [[optcell]]==0.
""",
@ -16135,7 +16135,7 @@ it is necessary to find the best set of preconditionning parameters
the default Pulay mixing is used).
* [[tfkinfunc]]=12: same as **tfkinfunc** =11, but without the initialization steps. Gradient correction is directly added.
* [[tfkinfunc]]=2: the Recursion Method is used in order to compute electronic density, entropy, Fermi energy and eigenvalues energy. This method computes the density without computing any orbital, is efficient at high temperature, with a efficient parallelization (almost perfect scalability). When that option is in use, the [[ecut]] input variable is no longer a convergence parameter ; [[ngfft]] becomes the main convergence parameter: you should adapt ecut for the ngfft grid you need (it is not yet automatically computed). Other convergence parameter are for the energetic values: [[recnrec]], [[recptrott]], [[recnpath]].
* [[tfkinfunc]]=2: the Recursion Method is used in order to compute electronic density, entropy, Fermi energy and eigenvalues energy. This method computes the density without computing any orbital, is efficient at high temperature, with a efficient parallelization (almost perfect scalability). When that option is in use, the [[ecut]] input variable is no longer a convergence parameter; [[ngfft]] becomes the main convergence parameter: you should adapt ecut for the ngfft grid you need (it is not yet automatically computed). Other convergence parameter are for the energetic values: [[recnrec]], [[recptrott]], [[recnpath]].
Since the convergence of the self-consistent cycle is determined directly by
the convergence of the density: [[toldfe]], [[toldff]], [[tolrff]],
[[tolvrs]], [[tolwfr]] are not used, and are replaced by [[rectolden]]; the
@ -18210,7 +18210,7 @@ Variable(
defaultval="[[AUTO_FROM_PSP]]",
mnemonics="WaveFunction OPTimisation ALGorithm",
characteristics=['[[DEVELOP]]'],
commentdefault="0 when [[usepaw]]=0 (norm-conserving pseudopotentials), 10 when [[usepaw]]=1 (PAW) ; 114 if [[paral_kgb]]=1.",
commentdefault="0 when [[usepaw]]=0 (norm-conserving pseudopotentials), 10 when [[usepaw]]=1 (PAW); 114 if [[paral_kgb]]=1.",
text="""
Allows one to choose the algorithm for the optimisation of the wavefunctions.
The different possibilities are:
@ -18219,7 +18219,7 @@ The different possibilities are:
* [[wfoptalg]]=2: minimisation of the residual with respect to different shifts, in order to cover the whole set of occupied bands, with possibility to parallelize over blocks of states (or bands). The number of states in a block is defined in [[nbdblock]]. THIS IS STILL IN DEVELOPMENT.
* [[wfoptalg]]=3: minimisation of the residual with respect to a shift. Available only in the non-self-consistent case [[iscf]]=-2, in order to find eigenvalues and wavefunctions close to a prescribed value.
* [[wfoptalg]]=4: (see also [[wfoptalg]]=14), a parallel code based on the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) method of Knyazev. [ Reference: A.V. Knyazev, "Toward the Optimal Preconditioned Eigensolver: Locally Optimal Block Preconditioned Conjugate Gradient Method". SIAM Journal on Scientific Computing 23, pp517-541 (2001) ](http://dx.doi.org/10.1137/S1064827500366124) . The implementation rests on the [ matlab program by Knyazev ](http://www.mathworks.com/matlabcentral/fileexchange/48-lobpcg-m) . [ Reference A. V. Knyazev, I. Lashuk, M. E. Argentati, and E. Ovchinnikov, Block Locally Optimal Preconditioned Eigenvalue Xolvers (BLOPEX) in hypre and PETSc (2007). SIAM Journal on Scientific Computing (SISC). 25(5): 2224-2239 ](http://dx.doi.org/10.1137/060661624) . For more information see [ F. Bottin, S. Leroux, A. Knyazev, G. Zerah, Large scale ab initio calculations based on three levels of parallelization. (2008). Computational Material Science, 42(2), 329-336. ](http://dx.doi.org/10.1016/j.commatsci.2007.07.019)
* [[wfoptalg]]=10: (for PAW) standard state-by-state conjugate gradient algorithm, with no possibility to parallelize over the states, but modified scheme described in Kresse, Furthmuller, PRB 54, 11169 (1996) (modified kinetic energy, modified preconditionning, minimal orthogonalization, ...) ;
* [[wfoptalg]]=10: (for PAW) standard state-by-state conjugate gradient algorithm, with no possibility to parallelize over the states, but modified scheme described in Kresse, Furthmuller, PRB 54, 11169 (1996) (modified kinetic energy, modified preconditionning, minimal orthogonalization, ...);
* [[wfoptalg]]=14: the recommended for parallel code, the same as [[wfoptalg]]=4 except that the preconditioning of the block vectors does not depend on the kinetic energy of each band, and the orthogonalization after the LOBPCG algorithm is no longer performed. The first modification increases the convergence and the second one the efficiency.
* [[wfoptalg]]=114: A new version of [[wfoptalg]]=14 which is more efficient for few blocks and can take advantage of OpenMP if abinit is compiled with a multithreaded linear algebra library. With more than 1 thread [[npfft]] shoud NOT be used for the time being.
* [[wfoptalg]]=1: new algorithm based on Chebyshev filtering, designed for very large number of processors, in the regime where LOBPCG does not scale anymore. It is not able to use preconditionning and therefore might converge slower than other algorithms. By design, it will **not** converge the last bands: it is recommended to use slightly more bands than necessary. For usage with [[tolwfr]], it is imperative to use [[nbdbuf]]. For more performance, try [[use_gemm_nonlop]]. For more information, see the [ performance guide ](../../theory/howto_chebfi.pdf) and the [ paper ](https://arxiv.org/abs/1406.4350) by A. Levitt and M. Torrent. Status: experimental but usable. Questions and bug reports should be sent to antoine (dot) levitt (at) gmail.com.

12
abimkdocs/website.py
View File

@ -344,17 +344,9 @@ class Website(object):
self.abinit_stats = AbinitStats(os.path.join(self.root, "maintainers", "statistics.txt"))
self.abinit_stats.json_dump(os.path.join(self.root, "developers", "statistics.json"))
# Build AbinitTestSuite object.
# Build flat list of tests.
from doc import tests as tmod
tests = []
for t in tmod.abitests.select_tests(suite_args=[], regenerate=True):
# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
# See https://stackoverflow.com/questions/9006740/isinstance-and-type-equivelence-failure-due-to-import-mechanism-python-djan
#if isinstance(t, ChainOfTests):
if hasattr(t, "tests"):
tests.extend(t.tests)
else:
tests.append(t)
tests = tmod.abitests.select_tests(suite_args=[], regenerate=True, flat_list=True)
# Construct dictionary rpath --> test. Use OrderedDict to have deterministic behaviour.
self.rpath2test = {}

40
abimkdocs_tests/test_variables.py
View File

@ -6,8 +6,10 @@ from .tools import patch_syspath, AbimkdocsTest
patch_syspath()
import os
from abimkdocs.variables import get_variables_code, ValueWithUnit, ValueWithConditions, MultipleValue, Range
import json
from collections import OrderedDict
from abimkdocs.variables import get_variables_code, ValueWithUnit, ValueWithConditions, MultipleValue, Range
class VariablesTest(AbimkdocsTest):
@ -91,25 +93,26 @@ class VariablesTest(AbimkdocsTest):
raise ValueError("\n".join(errors))
def test_variables_in_tests(self):
"""
Find variables that are not tested by comparing the database of variables
with the input file of the test.
Build dictionary with list of untested variables for the different codes.
Finally compare the new dictionary with the reference one and fail if they don't match.
"""
# Build database with all input variables indexed by code name.
from abimkdocs.variables import get_variables_code
variables_code = get_variables_code()
# Build AbinitTestSuite object.
from doc import tests as tmod
tests = tmod.abitests.select_tests(suite_args=[], regenerate=True, flat_list=True)
# Build conter for the different codes, keys are the varnames from the database.
from collections import Counter
count_code = {}
for code, d in variables_code.items():
count_code[code] = Counter({k: 0 for k in d})
# Build AbinitTestSuite object.
from doc import tests as tmod
tests = []
for t in tmod.abitests.select_tests(suite_args=[], regenerate=True):
# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
if hasattr(t, "tests"):
tests.extend(t.tests)
else:
tests.append(t)
black_list = set([
"atompaw", "cut3d", "multibinit", "fftprof", "conducti", "mrgscr",
"mrgddb", "mrggkk", "mrgdv", "band2eps", "ujdet", "fold2Bloch", "macroave",
@ -121,9 +124,10 @@ class VariablesTest(AbimkdocsTest):
#print(vnset)
count_code[test.executable].update(vnset)
untested = {}
untested = OrderedDict()
for code, count in count_code.items():
untested[code] = []
# Add it if var is not tested and not internal.
for vname, c in count.items():
if c == 0 and not variables_code[code][vname].is_internal:
print(code, vname)
@ -133,3 +137,15 @@ class VariablesTest(AbimkdocsTest):
untested[code] = sorted(untested[code])
print(code, untested[code])
#assert 0
ref_json_path = os.path.join(os.path.dirname(__file__), "untested_variables.json")
update_ref = False
if update_ref:
with open(ref_json_path, "wt") as fh:
json.dump(untested, fh, indent=4)
else:
with open(ref_json_path, "rt") as fh:
ref_untested = json.load(fh)
self.assertDictEqual(untested, ref_untested,
msg="Detected mismatch between reference file and new list of untested variables.")

76
doc/guide/abinit.md
View File

@ -174,17 +174,19 @@ before it and after it (again, multiple blanks are irrelevant).
ABINIT has also some (very limited) interpretor capabilities:
* It can identify one slash sign (/) being placed between two numbers
(without a separating blank) as being the definition of a fraction (e.g. 1/3 will be interpreted as 0.33333333333333d0) ;
(without a separating blank) as being the definition of a fraction
(e.g. 1/3 will be interpreted as 0.33333333333333d0);
* It can identify sqrt(...) or -sqrt(...) as being the definition of a square root,
when applied to one valid number - also without a separating blank - (e.g. -sqrt(0.75) will be interpreted as -0.8660254038d0) ;
when applied to one valid number - also without a separating blank -
(e.g. -sqrt(0.75) will be interpreted as -0.8660254038d0);
* Note, however, that these capabilities are NOT recursive.
At most, a sqrt identifier can contain an expression that uses a fraction (e.g. sqrt(3/4) is OK),
but two fractions (or two sqrt) cannot be used in one expression, and a sqrt cannot be present
in the numerator or denominator of a fraction.
Comments should be placed to the right of the comment characters # or ! ;
Comments should be placed to the right of the comment characters # or !;
anything to the right of a "#" or a "!" on any line is simply ignored by the
parser. Additional text, not preceded by a "#" or a "!" would not otherwise
cause trouble unless the text inadvertently contained character strings which
@ -206,9 +208,16 @@ the input variable is given: a **mnemonics**, possibly some
**characteristics**, the **variable type** (integer, real, string), and the
**default value**. Then, follows the description of the variable.
The **characteristics** can be one of the following: **DEVELOP**,
**NO_MULTI**, **INTERNAL_ONLY**, **INPUT_ONLY**, **EVOLVING**, **ENERGY**
, **LENGTH**, **MAGNETIC FIELD**, as described now.
The **characteristics** can be one of the following:
- **DEVELOP**,
- **NO_MULTI**
- **INTERNAL_ONLY**
- **INPUT_ONLY**
- **EVOLVING**
- **ENERGY**
- **LENGTH**
- **MAGNETIC FIELD**
#### Physical information
@ -219,23 +228,26 @@ can treat its physical dimensions with some units.
The use of the atomic unit system (e.g. the Hartree for energy, about 27.211
eV, and the Bohr for lengths about 0.529 Angstroms) is strictly enforced
within the code. However, the dimension of some input variables can be
specified and read correctly. At present, this applies to three types of
specified and read correctly.
At present, this applies to three types of
variables: those that have the dimension of an energy, those that have a
dimension of length, and those that have a dimension of magnetic field. The
first class of variables have the characteristics ' **ENERGY** ', and can be
specified in atomic units (Hartree), or electron-volts, or Rydbergs, or even
Kelvin. The second class of variables have the characteristics ' **LENGTH** ',
first class of variables have the characteristics **ENERGY**, and can be
specified in atomic units (Hartree), or electron-volts, or Rydbergs, or even Kelvin.
The second class of variables have the characteristics **LENGTH**,
and can be specified in atomic units (Bohr) and angstrom. The third class of
variables have the characteristics ' **MAGNETIC FIELD** ', and can be
variables have the characteristics **MAGNETIC FIELD**, and can be
specified in atomic units and Tesla. The abinit parser recognize a dimension
if it is specified after the list of numbers following the input variable
keyword, in the input file. The specification can be upper or lower case, or a
mix thereof. Here is the list of recognized chains of characters:
* 'Ry ' => Rydberg (for energies)
* 'eV ' => electron-volts (for energies)
* 'K ' => Kelvin (for energies)
* 'Angstr...' => Angstrom (for lengths)
* Ry --> Rydberg (for energies)
* eV --> electron-volts (for energies)
* K --> Kelvin (for energies)
* Angstr --> Angstrom (for lengths)
Except in the case of 'Angstr', the abbreviation must be used (i.e. 'Rydberg'
will not be recognized presently). Other character chains, like "au" (for
@ -263,15 +275,15 @@ even in reduced coordinates, through [[xred]].
Most of the variables can be used in the multi-dataset mode (see section 3.3),
but those that must have a unique value throughout all the datasets are
signaled with the indication ' **NO_MULTI** '.
signaled with the indication **NO_MULTI**.
Some of the input variables, with characteristics ' **INPUT_ONLY** ' are only
Some of the input variables, with characteristics **INPUT_ONLY** are only
used by the parser, to initialize other input variables, but are not
transmitted inside the code, beyond the parser. In particular, they are not
echoed in the output file.
At variance, some internal variables, with characteristics ' **INTERNAL_ONLY**
' are documented in the help files, but are not accessible as input variables.
At variance, some internal variables, with characteristics **INTERNAL_ONLY**
are documented in the help files, but are not accessible as input variables.
The documentation is provided because such variables are sometimes mentioned
in the output file.
@ -279,11 +291,11 @@ Most of the input variables do not change while a run is performed. Some of
them, by contrast, may evolve, like the atomic positions, the atomic
velocities, the cell shape, and the occupation numbers. Their echo, after the
run has proceeded, will of course differ from their input value. They are
signaled by the indication ' **EVOLVING** '.
signaled by the indication **EVOLVING**.
#### Other information
'**DEVELOP**' refers to input variables that are not used in production
**DEVELOP** refers to input variables that are not used in production
runs, but have been introduced during development time, of a feature that is
likely not finalized. For non ABINIT developers, it is strongly advised to skip them.
@ -492,17 +504,17 @@ is equivalent to
### 3.6 File names in the multi-dataset mode
The root names for input and output files (potential, density, wavefunctions
and so on) will receive an appendix: ' **_DS** ' followed by the index of the
and so on) will receive an appendix: **_DS** followed by the index of the
dataset. See section 4.
The ' **get** ' variables can be used to chain the calculations.
The **get** variables can be used to chain the calculations.
Let us mention a few of them: [[getwfk]], [[getwfq]], [[getddk]], [[get1wf]],
[[getden]], [[getcell]], [[getxred]] and [[getxcart]].
* [[getwfk]] allows to take the output wavefunctions of a previous dataset and use them as input wavefunctions
* [[getwfq]], [[getddk]] and [[get1wf]] do similar things for response function calculations
* [[getden]] does the same for the density ; [[getcell]] does the same for [[acell]] and [[rprim]]
* [[getden]] does the same for the density; [[getcell]] does the same for [[acell]] and [[rprim]]
* [[getxred]] and [[getxcart]] do the same for the atomic positions, either in reduced coordinates, or in cartesian coordinates.
The different variables corresponding to each dataset are echoed using the
@ -540,10 +552,10 @@ the record of the run in a nicer looking format.
**abi**
The other files READ by the code will have a name that is constructed from the
root "abi". This apply to optionally read wavefunction, density or potential
files. In the multi-dataset mode, this root will be complemented by ' **_DS**
' and the dataset index. The list of possible input files, with their name
created from the root 'abi', is the following (a similar list exist when '
**_DS** ' and the dataset index are appended to 'abi'):
files. In the multi-dataset mode, this root will be complemented by **_DS**
and the dataset index. The list of possible input files, with their name
created from the root 'abi', is the following (a similar list exist when
**_DS** and the dataset index are appended to 'abi'):
* **abi_WFK**
filename of file containing input wavefunction coefficients created from an
@ -578,11 +590,11 @@ filename of file containing an approximate hessian, for eventual
Except "ab_out" and "log", the other files WRITTEN by the code will have a
name that is constructed from the root "abo". This apply to optionally written
wavefunction, density, potential, or density of states files. In the multi-
dataset mode, this root will be complemented by ' **_DS** ' and the dataset
dataset mode, this root will be complemented by **_DS** and the dataset
index. Also in the multi-dataset mode, the root "abo" can be used to build the
name of **input** files, thanks to the 'get' variables. The list of possible
output files, with their name created from the root 'abo' is the following (a
similar list exists when ' **_DS** ' and the dataset index are appended to 'abo'):
similar list exists when **_DS** and the dataset index are appended to 'abo'):
* **abo_WFK**
Filename of file containing output wavefunction coefficients, if [[nqpt]]=0.
@ -924,7 +936,7 @@ following Fortran90 instructions (format 5.7):
& npwarr(1:nkpt),so_psp(1:npsp),symafm(1:nsym),symrel(1:3,1:3,1:nsym),typat(1:natom),&
& kpt(1:3,1:nkpt),occ(1:bantot),tnons(1:3,1:nsym),znucltypat(1:ntypat),wtk(1:nkpt)
do ipsp=1,npsp
! (npsp lines, 1 for each pseudopotential ; npsp=ntypat, except if alchemical pseudo-atoms)
! (npsp lines, 1 for each pseudopotential; npsp=ntypat, except if alchemical pseudo-atoms)
write(unit=unit) title,znuclpsp,zionpsp,pspso,pspdat,pspcod,pspxc,lmn_size
enddo
!(in case of usepaw==0, final record: residm, coordinates, total energy, Fermi energy)
@ -980,7 +992,7 @@ The format for version 4.4, 4.5, 4.6, 5.0, 5.1 and 5.2 was:
& npwarr(1:nkpt),so_typat(1:ntypat),symafm(1:nsym),symrel(1:3,1:3,1:nsym),typat(1:natom),&
& kpt(1:3,1:nkpt),occ(1:bantot),tnons(1:3,1:nsym),znucltypat(1:ntypat)
do ipsp=1,npsp
! (npsp lines, 1 for each pseudopotential ; npsp=ntypat, except if alchemical pseudo-atoms)
! (npsp lines, 1 for each pseudopotential; npsp=ntypat, except if alchemical pseudo-atoms)
write(unit=unit) title,znuclpsp,zionpsp,pspso,pspdat,pspcod,pspxc,lmn_size
enddo
!(in case of usepaw==0, final record: residm, coordinates, total energy, Fermi energy)

21
doc/installation.md
View File

@ -4,7 +4,7 @@ This file provides a description of the operations needed to install the
ABINIT package, to generate the executable and to make the tests.
It provides also the description of simple modifications of the package, for developers.
See a recent version of the [new user's guide](../users/new_user_guide.html),
See a recent version of the [new user's guide](guide/new_user.md),
for an introduction to the abinit package.
See a recent version of the [[help:abinit]] file for learning how to use the code.
Both of them can be found either on the Web, or in the doc subdirectory of the package.
@ -347,21 +347,15 @@ appropriate library to be installed in order to work properly.
For further information on these internal tests, see the ~abinit/tests/built-in/README file.
You might now read the [new user's guide](../users/new_user_guide.html), in
You might now read the [new user's guide](guide/new_user.md), in
order to learn how to use the code, and then to follow the four basic
tutorials, see the [entry page for the tutorials](../tutorial/welcome.html).
tutorials, see the [entry page for the tutorials](tutorial/index.md).
This is useful if you consider that the installation has been successful. Or
you might continue to read the present Web page, and try to perform the speed
tests, as well as the other tests.
## How to make the other tests?
Although it is possible to make the other tests without knowing really how to
use the code (since all steps involved - the run and subsequent analysis - are
done automatically), for the other tests, it is recommended to read the
[new user's guide](../users/new_user_guide.html), and then to follow the four basic
tutorials, see the [entry page for the tutorials](../tutorial/welcome.html).
Let us pursue with the testing procedure. Go to the ~abinit/tests directory, and issue:
make help
@ -411,8 +405,7 @@ used (automatically), possibly the other input files (like pseudopotentials),
the output files to be analyzed, the admitted tolerances with respect to
reference output files, the author of the test, and a brief description of the test.
To run only the tests in this directory, simply issue, in the ~abinit/tests/
directory:
To run only the tests in this directory, simply issue, in the ~abinit/tests/ directory:
./runtests.py fast
@ -472,8 +465,7 @@ differences in:
* the platform description (possibly);
* the overall execution time (this is ALWAYS printed, even without differences).
So, a successful execution of one test case may be announced as follows in the
fldiff.report file:
So, a successful execution of one test case may be announced as follows in the fldiff.report file:
Case_1
2
@ -491,8 +483,7 @@ fldiff.report file:
The fldiff.report file will have one such section for each test_case that was
run. It begins with the number of the test case, then includes a few blocks of
three lines: the number of the line where something is happening, followed by
the content of the two lines. Finally, there is a one-line summary for each
test case.
the content of the two lines. Finally, there is a one-line summary for each test case.
More information on the fldiff script can be found in the ~abinit/tests/Scripts/fldiff.pl file.

2
mksite.py
View File

@ -8,7 +8,7 @@ import warnings
import mkdocs.__main__
if sys.version_info < (3, 6):
warnings.warn("""Python >= 3.6 is STRONGLY recommended when building the Abinit documentation""")
warnings.warn("Python >= 3.6 is STRONGLY recommended when building the Abinit documentation\n" * 20)
# We don't install with setup.py hence we have to add the directory [...]/abinit/tests to $PYTHONPATH
pack_dir = os.path.dirname(os.path.abspath(__file__))

25
tests/__init__.py
View File

@ -726,19 +726,16 @@ class AbinitTests(object):
return d
def select_tests(self, suite_args, regenerate=False, keys=None,
authors=None, ivars=None, with_pickle=True):
authors=None, ivars=None, with_pickle=True, flat_list=False):
"""
Main entry point for client code.
Return an instance of AbinitTestSuite
Main entry point for client code. Return an instance of AbinitTestSuite
Args:
with_pickle:
Save the generated database in pickle format.
with_pickle: Save the generated database in pickle format.
flat_list: True if a flat list of tests should be returned instead
of a list that can contain ChainOfTests objects.
"""
try:
tests_todo = self._suite_args_parser(suite_args)
except:
raise
# Load the full database.
database = self.get_database(regenerate=regenerate, with_pickle=with_pickle)
@ -797,7 +794,19 @@ class AbinitTests(object):
exclude_authors=exclude_authors,
ivars=ivars
)
if not flat_list:
return tests
else:
# Build flat list of tests.
flat = []
for t in tests:
if isinstance(t, ChainOfTests):
# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
#if hasattr(t, "tests"):
flat.extend(t.tests)
else:
flat.append(t)
return flat
def generate_html_listoftests(self):
"""Generate the ListOfTests files"""