# BerkeleyGW manual (version 1.1 beta)

## Contents

This manual is assembled automatically from the various documentation files in the BerkeleyGW distribution. The headings are the paths and filenames. For each executable, consult the corresponding .inp file for information about input parameters. The homepage is http://www.berkeleygw.org.

## Preliminaries


BerkeleyGW, Copyright (c) 2011, The Regents of the University of
California, through Lawrence Berkeley National Laboratory (subject to
receipt of any required approvals from the U.S. Dept. of Energy).

If you have questions about your rights to use or distribute this
at  TTD@lbl.gov.

NOTICE.  This software was developed under partial funding from the
U.S. Department of Energy.  As such, the U.S. Government has been
granted for itself and others acting on its behalf a paid-up,
nonexclusive, irrevocable, worldwide license in the Software to
reproduce, prepare derivative works, and perform publicly and display
publicly.  Beginning five (5) years after the date permission to
assert copyright is obtained from the U.S. Department of Energy, and
subject to any subsequent five (5) year renewals, the U.S. Government
is granted for itself and others acting on its behalf a paid-up,
nonexclusive, irrevocable, worldwide license in the Software to
reproduce, prepare derivative works, distribute copies to the public,
perform publicly and display publicly, and to permit others to do so.

-------------------------------------------------------

BerkeleyGW - The Berkeley GW (And More) Package
http://www.berkeleygw.org

Version 1.1   (June, 2014)

Version 1.0	(Aug, 2011)
J. Deslippe, G. Samsonidze, D. A. Strubbe, M. Jain

Version 0.5	(July, 2008)
J. Deslippe, G. Samsonidze, L. Yang, F. Ribeiro

Version 0.2	M. L. Tiago	(2001)	Original BSE Code, PlotXct
S. Ismail-Beigi	(2002)	FFT, Documentation, General Improvements
C. Spataru	(2005)	Cylindrical Coulomb Truncation, Transform (obsolete)
Version 0.1	X. Blase	(1998)	Implemented F90, Preprocessing, Dynamical Memory Allocation
G. M. Rignanese				"		"
E. Chang				"		"
Version 0.0	M. Hybertsen	(1985)	Original GW Code

To report current bugs or problems, contact Jack Deslippe: jdeslip@civet.berkeley.edu

------------------------------------------------------

See more details in the README and .inp files in individual directories.

------------------------------------------------------

Compilation
-----------

We have tested the code extensively with various configurations, and support the following compilers and libraries:
* Operating systems: Linux, AIX, MacOS
* Fortran compilers (required): pgf90, ifort, gfortran, g95, openf90, sunf90, pathf90, crayftn, af90 (Absoft), nagfor, xlf90 (experimental)
* C compilers (optional): pgcc, icc, gcc, opencc, pathcc, craycc, clang
* C++ compilers (optional): pgCC, icpc, g++, openCC, pathCC, crayCC, clang++
* MPI implementation (optional): OpenMPI, MPICH1, MPICH2, MVAPICH2, Intel MPI
* LAPACK/BLAS implementation (required): NetLib, ATLAS, Intel MKL, ACML, Cray LibSci
* ScaLAPACK/BLACS implementation (required by BSE if MPI is used): NetLib, Cray LibSci, Intel MKL, AMD
* FFTW (required): versions 2.1.5.x

1. Architecture-specific Makefile-include files appropriate for various supercomputers as well as
for using standard Ubuntu or Macports packages are provided in the config directory. Copy or
link one to the top directory. Example:

cp config/lonestar.tacc.utexas.edu.mk arch.mk

2. Edit it to fit your needs. Refer to config/README for details.

3. Copy flavor_real.mk or flavor_cplx.mk to flavor.mk to set flavor.
Complex may always be used. Real may be used for systems that
have both inversion (about the origin) and time-reversal symmetry, and will be
faster and use less memory.

4. Stay in the root directory and run the following commands
to compile the various codes:

MAIN:
make epsilon
make epsilon-all               Epsilon + utilities
make sigma
make sigma-all                 Sigma + utilities
make bse
make bse-all                   BSE + utilities

MISC:
make plotxct
make meanfield
make epm
make sapo
make siesta2bgw
make bgw2para
make kgrid
make icm
make surface

EVERYTHING:
make all                       All codes/packages (for selected flavor)
make -j all                    parallel build (for selected flavor)
make all-flavors               everything, for both flavors
make -j all-flavors            parallel build of everything, for both flavors
make install INSTDIR=          install binaries, library, examples, testsuite into specified prefix

These commands will generate executables with extension .x in
the source directory and symbolic links with the same name in
the bin directory.

Development
-----------
Spirit of contributions:

1. These codes are to be used on various machine architectures
employing various compilers and libraries. Therefore, try not
to write machine-specific code or quick fixes that will have to
be reversed later.
2. Limit compilation changes as much as possible to arch.mk and ensure
that this is suitable for all codes in Epsilon/, Sigma/, and BSE/.
Hopefully individual Makefiles will only require the addition of
new source-code files.
3. Test the codes using the examples/ and please augment the examples/
with your own test cases (provided they are not too computationally
expensive).


Unless otherwise stated, all files distributed in this package
are licensed under the following terms.

BerkeleyGW, Copyright (c) 2011, The Regents of the University of
California, through Lawrence Berkeley National Laboratory (subject to
receipt of any required approvals from the U.S. Dept. of Energy).

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

(1) Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.

(2) Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

(3) Neither the name of the University of California, Lawrence
Berkeley National Laboratory, U.S. Dept. of Energy nor the names of
its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

You are under no obligation whatsoever to provide any bug fixes,
patches, or upgrades to the features, functionality or performance of
the source code ("Enhancements") to anyone; however, if you choose to
make your Enhancements available either publicly, or directly to
Lawrence Berkeley National Laboratory, without imposing a separate
written license agreement for such Enhancements, then you hereby grant
the following license: a  non-exclusive, royalty-free perpetual
license to install, use, modify, prepare derivative works, incorporate
into other computer software, distribute, and sublicense such
enhancements or derivative works thereof, in binary and source code
form.


## CONTRIBUTORS

Brad A. Barker (BAB)
Xavier Blase (XAV)
Andrew Canning (AC)
Eric K. Chang (EKC)
Sangkook Choi (SKC)
Jack R. Deslippe (JRD)
Peter W. Doak (PWD)
Mark S. Hybertsen (MSH)
Sohrab Ismail-Beigi (SIB)
Manish Jain (MJ)
Je-Luen Li (JLL)
Andrei S. Malashevich (ASM)
Jamal I. Mustafa (JIM)
Jeffrey B. Neaton (JBN)
Cheol-Hwan Park (CHP)
David G. Prendergast (DGP)
Filipe J. Ribeiro (FJR)
Gian-Marco Rignanese (GMR)
Georgy Samsonidze (GSM)
Catalin D. Spataru (CDS)
David A. Strubbe (DAS)
Murilo L. Tiago (MLT)
Derek W. Vigil (DWV)
Li Yang (LY)
Oleg V. Yazyev (OVY)
Peihong Zhang (PZ)


## LITERATURE.html

Please let us know when your paper is published with BerkeleyGW for inclusion here (or any other additions or corrections) in the Forum, under the "Literature" topic.

I. Papers on the implementation of BerkeleyGW
1. Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, "BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures," Comput. Phys. Commun. 183, 1269 (2012) (most up-to-date on arXiV)
2. Mark S. Hybertsen and Steven G. Louie, "Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies," Phys. Rev. B 34, 5390 (1986) [GW, GPP, COHSEX] Errata: Eq. 11 should have E' instead of E in the numerator. Eq. 32 should have Ω2 rather than Ω in the numerator. Eq. 34a should have δG,G instead of 1 in the parentheses.
3. Sheng Bai Zhang, David Tománek, Marvin L. Cohen, Steven G. Louie, and Mark S. Hybertsen, "Evaluation of quasiparticle energies for semiconductors without inversion symmetry," Phys. Rev. B 40, 3162 (1989) [GPP for systems without inversion symmetry]
4. Michael Rohlfing and Steven G. Louie, "Electron-hole excitations and optical spectra from first principles," Phys. Rev. B 62, 4927 (2000) [BSE] Errata: Eqs. 26 and 27 should have 8π2 instead of 16π in the prefactor. Eq. 44 should be a sum over G ≠ 0. Eq. 45 should have ε-1G,G' instead of ε-1G,0.
5. Je-Luen Li, Gian-Marco Rignanese, Eric K. Chang, Xavier Blase, and Steven G. Louie, "GW study of the metal-insulator transition of bcc hydrogen," Phys. Rev. B 66, 035102 (2002) [spin-polarized GW]
6. Sohrab Ismail-Beigi, "Truncation of periodic image interactions for confined systems," Phys. Rev. B 73, 233103 (2006) [slab and wire truncation]
7. Jeffrey B. Neaton, Mark S. Hybertsen, and Steven G. Louie, "Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces," Phys. Rev. Lett. 97, 216405 (2006) [ICM] Erratum: p. 3, left col, last paragraph. Should be 1/2|z-z0| instead of 1/4|z-z0|.
8. R. Haydock, "The recursive solution of the Schrödinger equation," Comput. Phys. Commun. 20, 11 (1980)
9. Loren X. Benedict and Eric L. Shirley, "Ab initio calculation of ε2(ω) including the electron-hole interaction: Application to GaN and CaF2," Phys. Rev. B 59, 5441 (1999) [Haydock recursion in BSE]
10. Georgy Samsonidze, Manish Jain, Jack Deslippe, Marvin L. Cohen, and Steven G. Louie, "Simple approximate physical orbitals for GW quasiparticle calculations," Phys. Rev. Lett. 107, 186404 (2011) [SAPO]
II. Review articles on the GW approximation and Bethe-Salpeter equation approaches
1. Lars Hedin and Stig Lundqvist, "Effects of Electron-Electron and Electron-Phonon Interactions on the One-Electron States of Solids," Solid State Phys. 23, 1 (1970)
2. Mark S. Hybertsen and Steven G. Louie, "Theory and Calculation of Quasiparticle Energies and Band Gaps," Comments on Cond. Mat. Phys. 13, 223 (1987)
3. G. Strinati, "Application of the Green's functions method to the study of the optical properties of semiconductors," Riv. Nuovo Cimento 11, 1 (1988)
4. Steven G. Louie, "Quasiparticle Theory of Electron Excitations in Solids," in Quantum Theory of Real Materials, eds. James R. Chelikowsky and Steven G. Louie, (Kluwer Press, Boston, 1996), p. 83
5. Steven G. Louie, "First-Principles Theory of Electron Excitation Energies in Solids, Surfaces, and Defects," in Topics in Computational Materials Science, ed. Ching-Yao Fong (World Scientific, Singapore, 1998) p. 96
6. F. Aryasetiawan and O. Gunnarsson, "The GW method," Rep. Prog. Phys. 61, 237 (1998)
7. Lars Hedin, "On correlation effects in electron spectroscopies and the GW approximation," J. Phys.: Condens. Matter 11, R489 (1999)
8. Wilfried G. Aulbur, Lars Jönsson, and John W. Wilkins, "Quasiparticle calculations in solids," Solid State Phys. 54, 1 (1999)
9. Giovanni Onida, Lucia Reining, and Angel Rubio, "Electronic excitations: density-functional versus many-body Green's-function approaches," Rev. Mod. Phys. 74, 601 (2002)
10. Steven G. Louie, "Predicting Materials and Properties: Theory of the Ground and Excited State," in Conceptual Foundations of Materials: A Standard Model for Ground- and Excited-State Properties, vol. eds. Steven G. Louie and Marvin L. Cohen (Elsevier, Amsterdam, 2006) p. 9
III. Papers using BerkeleyGW
1. Mark S. Hybertsen and Steven G. Louie, "First Principles Theory of Quasiparticles: Calculation of Band Gaps in Semiconductors and Insulators," Phys. Rev. Lett. 55, 1418 (1985)
2. Mark S. Hybertsen and Steven G. Louie, "Electron Correlation and the Band Gap in Ionic Crystals," Phys. Rev. B 32, 7005(R) (1985) [Erratum: Phys. Rev. B 35, 9308 (1987)]
3. Mark S. Hybertsen and Steven G. Louie, "Many-body Calculation of Surface States: As on Ge(111)," Phys. Rev. Lett. 58, 1551 (1987)
4. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Theory of Quasiparticle Energies in Alkali Metals," Phys. Rev. Lett. 59, 819 (1987)
5. Steven G. Louie and Mark S. Hybertsen, "Theory of Quasiparticle Energies: Band Gaps and Excitation Spectra in Solids," Int. J. Quant. Chem.: Quant. Chem. Symp. 21, 31 (1987)
6. Sheng Bai Zhang, David Tománek, Steven G. Louie, Marvin L. Cohen, and Mark S. Hybertsen, "Quasiparticle Calculation of Valence Band Offset of AlAs-GaAs(001)," Solid State Comm. 66, 585 (1988)
7. Mark S. Hybertsen and Steven G. Louie, "Theory of Quasiparticle Surface States in Semiconductor Surfaces," Phys. Rev. B 38, 4033 (1988)
8. Michael P. Surh, John E. Northrup, and Steven G. Louie, "Occupied Quasiparticle Bandwidth of Potassium," Phys. Rev. B 38, 5976 (1988)
9. Xuejun Zhu, Stephen Fahy, and Steven G. Louie, "Ab Initio Calculation of Pressure Coefficients of Band Gaps of Silicon: Comparison of the Local-Density Approximation and Quasiparticle Results," Phys. Rev. B 39, 7840 (1989) [Erratum: Phys. Rev. B 40, 5821 (1989)]
10. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Quasiparticle excitation spectrum for nearly-free-electron metals," Phys. Rev. B 39, 8198 (1989)
11. Sheng Bai Zhang, David Tománek, Marvin L. Cohen, Steven G. Louie, and Mark S. Hybertsen, "Evaluation of Quasiparticle Energies for Semiconductors without Inversion Symmetry," Phys. Rev. B 40, 3162 (1989)
12. Sheng Bai Zhang, Mark S. Hybertsen, Marvin L. Cohen, Steven G. Louie, and David Tománek, "Quasiparticle Band Gaps for Ultrathin GaAs/AlAs(001) Superlattices," Phys. Rev. Lett. 63, 1495 (1989)
13. Xuejun Zhu, Sheng Bai Zhang, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle Interpretation of Photoemission Spectra and Optical Properties of GaAs(110)," Phys. Rev. Lett. 63, 2112 (1989)
14. Sheng Bai Zhang, Marvin L. Cohen, Steven G. Louie, David Tománek, and Mark S. Hybertsen, "Quasiparticle Band Offset at the (001) Interface and Band Gaps in Ultrathin Superlattices of GaAs-AlAs Heterojunctions," Phys. Rev. B 41, 10058 (1990)
15. Hélio Chacham, Xuejun Zhu, and Steven G. Louie, "Metal-Insulator Transition in Solid Xenon at High Pressures," Europhys. Lett. 14, 65 (1991)
16. Hélio Chacham and Steven G. Louie, "Metallization of Solid Hydrogen at Megabar Pressures: A First-Principles Quasiparticle Study," Phys. Rev. Lett. 66, 64 (1991)
17. John E. Northrup, Mark S. Hybertsen, and Steven G. Louie, "Many-Body Calculation of the Surface State Energies for Si(111)2×1," Phys. Rev. Lett. 66, 500 (1991)
18. Michael P. Surh, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle Energies for Cubic BN, BP, and BAs," Phys. Rev. B 43, 9126 (1991)
19. Xuejun Zhu and Steven G. Louie, "Quasiparticle Surface Band Structure and Photoelectric Threshold of Ge(111)-2×1," Phys. Rev. B 43, 12146(R) (1991)
20. Xuejun Zhu and Steven G. Louie, "Quasiparticle Band Structure of Thirteen Semiconductors and Insulators," Phys. Rev. B 43, 14142 (1991)
21. Michael P. Surh, Steven G. Louie, and Marvin L. Cohen, "Band Gaps of Diamond under Anisotropic Stress," Phys. Rev. B 45, 8239 (1992)
22. Hélio Chacham, Xuejun Zhu, and Steven G. Louie, "Pressure-Induced Insulator-Metal Transitions in Solid Xenon and Hydrogen: A First-Principles Quasiparticle Study," Phys. Rev. B 46, 6688 (1992) [Erratum: Phys. Rev. B 48, 2025(E) (1993)]
23. Eric L. Shirley, Xuejun Zhu, and Steven G. Louie, "Core-Polarization in Semiconductors: Effects on Quasiparticle Energies," Phys. Rev. Lett. 69, 2955 (1992)
24. Eric L. Shirley and Steven G. Louie, "Electron Excitations in Solid C60: Energy Gap, Band Dispersions, and Effects of Orientational Disorder," Phys. Rev. Lett. 71, 133 (1993)
25. Angel Rubio, Jennifer L. Corkill, Marvin L. Cohen, Eric L. Shirley, and Steven G. Louie, "Quasiparticle Band Structure of AlN and GaN," Phys. Rev. B 48, 11810 (1993)
26. Steven G. Louie and Eric L. Shirley, "Electron Excitation Energies in Fullerites: Many-Electron and Molecular Orientational Effects," J. Phys. Chem. Solids 54, 1767 (1993)
27. Xavier Blase, Xuejun Zhu, and Steven G. Louie, "Self-Energy Effects on the Surface State Energies of H-Si(111) 1×1," Phys. Rev. B 49, 4973 (1994)
28. J. A. Carlisle, L. J. Terminello, A. V. Hamza, E. A. Hudson, Eric L. Shirley, F. J. Himpsel, D. A. Lapiano-Smith, J. J. Jia, T. A. Callcott, R. C. C. Perera, D. K. Shuh, Steven G. Louie, J. Stöhr, M. G. Samant, and D. L. Ederer, "Occupied and Unoccupied Orbitals of C60 and C70," Mol. Cryst. Liq. Cryst. 256, 819 (1994)
29. Oleg Zakharov, Angel Rubio, Xavier Blase, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Band Structures of Six II-VI Compounds: ZnS, ZnSe, ZnTe, CdS, CdSe, and CdTe," Phys. Rev. B 50, 10780 (1994)
30. Xavier Blase, Angel Rubio, Steven G. Louie, and Marvin L. Cohen, "Quasiparticle band structure of bulk hexagonal boron nitride and related systems," Phys. Rev. B 51, 6868 (1995)
31. Michael P. Surh, Hélio Chacham, and Steven G. Louie, "Quasiparticle Excitation Energies for the F-Center Defect in LiCl," Phys. Rev. B. 51, 7464 (1995)
32. Eric L. Shirley and Steven G. Louie, "Photoemission and Optical Properties of C60 Fullerites," in Quantum Theory of Real Materials, eds. J.R. Chelikowsky and Steven G. Louie (Kluwer Press, Boston, 1996), p. 515.
33. Balazs Králik, Eric K. Chang, and Steven G. Louie, "Structural Properties and Quasiparticle Band Structure of Zirconia," Phys. Rev. B 57, 7027 (1998)
34. Michael Rohlfing and Steven G. Louie, "Electron-hole Excitations in Semiconductors and Insulators," Phys. Rev. Lett. 81, 2312 (1998)
35. Michael Rohlfing and Steven G. Louie, "Optical Excitations in Conjugated Polymers," Phys. Rev. Lett. 82, 1959 (1999)
36. Michael Rohlfing and Steven G. Louie, "Excitons and Optical Spectrum of the Si(111)-(2×1) Surface," Phys. Rev. Lett. 83, 856 (1999)
37. Eric K. Chang, Michael Rohlfing, and Steven G. Louie, "Excitons and Optical Properties of Alpha-Quartz," Phys Rev. Lett. 85, 2613 (2000)
38. Eric K. Chang, Michael Rohlfing, and Steven G. Louie, "First-Principles Study of Optical Excitations in Alpha-Quartz," in The Optical Properties of Materials, MRS Symp. Proceed. Vol. 579, eds. Eric L. Shirley, James R. Chelikowsky, Steven G. Louie, and Gérard Martinez (Materials Research Society, Warrendale, 2000), p. 3
39. Peihong Zhang, Vincent H. Crespi, Eric K. Chang, Steven G. Louie, and Marvin L. Cohen, "Computational Design of Direct-Bandgap Semiconductors that Lattice-Match Silicon," Nature 409, 69 (2001)
40. Jeffrey C. Grossman, Michael Rohlfing, Lubos Mitas, Steven G. Louie, and Marvin L. Cohen, "High Accuracy Many-Body Calculational Approaches for Excitations in Molecules," Phys. Rev. Lett. 86, 472 (2001)
41. Gian-Marco Rignanese, Xavier Blase, and Steven G. Louie, "Quasiparticle Effects on Tunneling Currents: A Study of C2H4 Adsorbed on the Si(001)-(2×1) Surface," Phys. Rev. Lett. 86, 2110 (2001)
42. Eric K. Chang, Xavier Blase, and Steven G. Louie, "Quasiparticle Band Structure of Lanthanum Hydride," Phys. Rev. B 64, 155108 (2001)
43. Catalin D. Spataru, M. A. Cazalilla, Angel Rubio, Loren X. Benedict, Pedro M. Echenique, and Steven G. Louie, "Anomalous Quasiparticle Lifetime in Graphite: Band Structure Effects," Phys. Rev. Lett. 87, 246405 (2001)
44. Je-Luen Li, Gian-Marco Rignanese, Eric K. Chang, Xavier Blase, and Steven G. Louie, "GW Study of the Metal-Insulator Transition of bcc Hydrogen," Phys. Rev. B 66, 035102 (2002)
45. Weidong Luo, Sohrab Ismail-Beigi, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Band Structure of ZnS and ZnSe," Phys. Rev. B 66, 195215 (2002)
46. Loren X. Benedict, Catalin D. Spataru, and Steven G. Louie, "Quasiparticle Properties of a Simple Metal at High Electron Temperatures," Phys. Rev. B 66, 085116 (2002)
47. J. A. Alford, Mei-Yin Chou, Eric K. Chang, and Steven G. Louie, "First-principles Studies of Quasiparticle Band Structures of Cubic YH3 and LaH3," Phys. Rev. B 67, 125110 (2003)
48. Murilo L. Tiago, John E. Northrup, and Steven G. Louie, "Ab initio calculation of the electronic and optical properties of solid pentacene," Phys. Rev. B 67, 11 5212 (2003)
49. Sohrab Ismail-Beigi and Steven G. Louie, "Excited-State Forces within a First-Principles Green's Function Formalism," Phys. Rev. Lett. 90, 076401 (2003)
50. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Excitonic effects and optical spectra of single-walled carbon nanotubes," Phys. Rev. Lett. 92, 077402 (2004)
51. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Quasiparticle energies, excitonic effects and optical absorption spectra of small-diameter single-walled carbon nanotubes," Appl. Phys. A 78, 1129 (2004)
52. Murilo L. Tiago, Sohrab Ismail-Beigi, and Steven G. Louie, "Effect of Semicore Orbitals on the Electronic Band Gaps of Si, Ge, and GaAs Within the GW Approximation," Phys. Rev. B 69, 125212 (2004)
53. Catalin D. Spataru, Loren X. Benedict, and Steven G. Louie, "Ab Initio Calculation of Band-Gap Renormalization in Highly Excited GaAs," Phys. Rev. B 69, 205204 (2004)
54. Murilo L. Tiago, Michael Rohlfing, and Steven G. Louie, "Bound Excitons and Optical Properties of Bulk Trans-Polyacetylene," Phys. Rev. B 70, 193204 (2004)
55. Je-Luen Li, Gian-Marco Rignanese, and Steven G. Louie, "Quasiparticle Energy Bands of NiO in the GW Approximation," Phys. Rev B 71, 193102 (2005)
56. Catalin D. Spataru, Sohrab Ismail-Beigi, Loren X. Benedict, and Steven G. Louie, "Excitonic Effects and Optical Spectra of Single-Walled Carbon Nanotubes," 27th Conference on the Physics of Semiconductors, AIP Conference Proceedings 772, 1061 (2005)
57. Jeffrey B. Neaton, Koonghong Khoo, Catalin D. Spataru, and Steven G. Louie, "Electronic Transport and Optical Properties of Carbon Nanostructures from First Principles," Comput. Phys. Commun. 169, 1 (2005)
58. Sohrab Ismail-Beigi and Steven G. Louie, "Self-Trapped Excitons in Silicon Dioxide: Mechanism and Properties," Phys. Rev. Lett. 95, 156401 (2005)
59. Catalin D. Spataru, Sohrab Ismail-Beigi, Rodrigo B. Capaz, and Steven G. Louie, "Theory and Ab Initio Calculation of Radiative Lifetime of Excitons in Semiconducting Carbon Nanotubes," Phys. Rev. Lett. 95, 247402 (2005)
60. Steven G. Louie and Angel Rubio, "Quasiparticle and Optical Properties of Solids and Nanostructures: The GW-BSE Approach," Handbook of Materials Modeling, ed. S. Yip (Springer, Dordrecht, The Netherlands, 2005), p. 215
61. Cheol-Hwan Park, Catalin D. Spataru, and Steven G. Louie, "Excitons and Many-Electron Effects in the Optical Response of Single-Walled Boron Nitride Nanotubes," Phys. Rev. Lett. 96, 126105 (2006)
62. Jeffrey B. Neaton, Mark S. Hybertsen, and Steven G. Louie, "Renormalization of Molecular Electronic Levels at Metal-Molecule Interfaces," Phys. Rev. Lett. 97, 216405 (2006)
63. Su Ying Quek, Jeffrey B. Neaton, Mark S. Hybertsen, E. Kaxiras, and Steven G. Louie, "First-principles Studies of the Electronic Structure of Cyclopentene on Si(001): Density Functional Theory and GW Calculations," Phys. Status Solidi (b) 243, 2048 (2006)
64. Rodrigo B. Capaz, Catalin D. Spataru, Sohrab Ismail-Beigi, and Steven G. Louie, "Diameter and Chirality Dependence of Exciton Properties in Carbon Nanotubes," Phys. Rev. B 74, 121401 (2006)
65. Takashi Miyake, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Energy of Semicore d-electrons in ZnS: Combined LDA+U and GW approach," Phys. Rev. B 74, 245213 (2006)
66. Li Yang, Catalin D. Spataru, Steven G. Louie, and Mei-Yin Chou, "Enhanced Electron-hole Interaction and Optical Absorption in a Silicon Nanowire," Phys. Rev. B 75, 201304(R) (2007)
67. Li Yang, Cheol-Hwan Park, Young-Woo Son, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle Energies and Band Gaps of Graphene Nanoribbons," Phys. Rev. Lett. 99, 186801 (2007)
68. Li Yang, Marvin L. Cohen, and Steven G. Louie, "Excitonic Effects in the Optical Spectra of Graphene Nanoribbons," Nano Lett. 7, 3112 (2007)
69. Feng Wang, David J. Cho, Brian Kessler, Jack Deslippe, P. James Schuck, Steven G. Louie, Alex Zettl, Tony F. Heinz, and Y. Ron Shen, "Observation of Excitons in One-Dimensional Metallic Single-Walled Carbon Nanotubes," Phys. Rev. Lett. 99, 227401 (2007)
70. Su Ying Quek, Jeffrey B. Neaton, Mark S. Hybertsen, Efthimios Kaxiras, and Steven G. Louie, "Negative Differential Resistance in Transport through Organic Molecules on Silicon," Phys. Rev. Lett. 98, 066807 (2007)
71. Catalin D. Spataru, Sohrab Ismail-Beigi, Rodrigo B. Capaz, and Steven G. Louie, "Quasiparticle and Excitonic Effects in the Optical Response of Nanotubes and Nanoribbons," in Carbon Nanotubes: Advanced Topics in the Synthesis, Structure, Properties and Applications, A. Jorio, M. S. Dresselhaus, G. Dresselhaus (eds.), Topics in Applied Physics 111 (Springer-Verlag, Heidelberg, Germany 2008), p. 195
72. Jack Deslippe, Catalin D. Spataru, David Prendergast, and Steven G. Louie, "Bound excitons in metallic single-walled carbon nanotubes," Nano Lett. 7, 1626 (2007)
73. Cheol-Hwan Park, Feliciano Giustino, Marvin L. Cohen, and Steven G. Louie, "Velocity Renormalization and Carrier Lifetime in Graphene from the Electron-Phonon Interaction," Phys. Rev. Lett. 99, 086804 (2007)
74. Brad D. Malone, Jay D. Sau, and Marvin L. Cohen, "Ab initio survey of the electronic structure of tetrahedrally bonded phases of silicon," Phys. Rev. B 78, 035210 (2008)
75. Jack Deslippe and Steven G. Louie, "Excitons and Many-electron Effects in the Optical Response of Carbon Nanotubes and Other One-dimensional Nanostructures," Proc. SPIE 6892, 68920U-1 (2008)
76. Emmanouil Kioupakis, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "GW Quasiparticle Corrections to the LDA+U/GGA+U Electronic Structure of bcc Hydrogen," Phys. Rev. B 77, 155114 (2008)
77. Jay D. Sau, Jeffrey B. Neaton, Hyoung Joon Choi, Steven G. Louie, and Marvin L. Cohen, "Electronic Energy Levels of Weakly Coupled Nanostructures: C60 Metal Interfaces," Phys. Rev. Lett. 101, 026804 (2008)
78. Li Yang, Marvin L. Cohen, and Steven G. Louie, "Magnetic Edge-state Excitons in Zigzag Graphene Nanoribbons," Phys. Rev. Lett. 101, 186401 (2008)
79. Cheol-Hwan Park, Feliciano Giustino, Jessica L. McChesney, Aaron Bostwick, Taisuke Ohta, Eli Rotenberg, Marvin L. Cohen, and Steven G. Louie, "Van Hove Singularity and Apparent Anisotropy in the Electron-phonon Interaction in Graphene," Phys. Rev. B 77, 113410 (2008)
80. Cheol-Hwan Park, Feliciano Giustino, Marvin L. Cohen, and Steven G. Louie, "Electron-phonon Interactions in Graphene, Bilayer Graphene, and Graphite," Nano Lett. 8, 4229 (2008)
81. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "First-principles Study of Electron Linewidths in Graphene," Phys. Rev. Lett. 102, 076803 (2009) [Erratum: Phys. Rev. Lett. 102, 189904(E) (2009)]
82. Jack Deslippe, Mario Dipoppa, David Prendergast, M. V. O. Moutinho, Rodrigo B. Capaz, and Steven G. Louie, "Electron-hole Interaction in Carbon Nanotubes: Novel Screening and Exciton Excitation Spectra," Nano Lett. 9, 1330 (2009)
83. Li Yang, Jack Deslippe, Cheol-Hwan Park, Marvin L. Cohen, and Steven G. Louie, "Excitonic effects on the optical response of graphene and bilayer graphene," Phys. Rev. Lett. 103, 186802 (2009)
84. Chenggang Tao, J. Sun, X. Zhang, Ryan Yamachika, Daniel Wegner, Yasaman Bahri, Georgy Samsonidze, Marvin L. Cohen, Steven G. Louie, T. Don Tilley, Rachel A. Segalman, and Michael F. Crommie, "Spatial resolution of a type II heterojunction in a single bipolar molecule," Nano Lett. 9, 3963 (2009)
85. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "Angle-resolved Photoemission Spectra of Graphene from First-principles," Nano Lett. 9, 4234 (2009)
86. Emmanouil Kioupakis, Murilo L. Tiago, and Steven G. Louie, "Quasiparticle electronic structure of bismuth telluride in the GW approximation," Phys. Rev. B 82, 245203 (2010)
87. Feliciano Giustino, Steven G. Louie, and Marvin L. Cohen, "Electron-phonon renormalization of the direct band gap of diamond," Phys. Rev. Lett. 105, 265501 (2010)
88. Brad D. Malone, Steven G. Louie, and Marvin L. Cohen, "Electronic and optical properties of body-centered-tetragonal Si and Ge," Phys. Rev. B 81, 115201 (2010)
89. Bi-Ching Shih, Yu Xue, Peihong Zhang, Marvin L. Cohen, and Steven G. Louie, "Quasiparticle band gap of ZnO: High accuracy from the conventional G0W0 approach," Phys. Rev. Lett. 105, 146401 (2010)
90. Victor W. Brar, Sebastian Wickenburg, Melissa Panlasigui, Cheol-Hwan Park, Tim O. Wehling, Yuanbo Zhang, R. Decker, Caglar Girit, A. V. Balatsky, Steven G. Louie, Alex Zettl, and Michael F. Crommie, "Observation of Carrier-Density-Dependent Many-Body Effects in Graphene via Tunneling Spectroscopy," Phys. Rev. Lett. 104, 036805 (2010)
91. G. S. Do, J. Kim, Seung-Hoon Jhi, Cheol-Hwan Park, Steven G. Louie, and Marvin L. Cohen, "Ab Initio Calculations of Pressure-induced Structural Phase Transitions of GeTe," Phys. Rev. B 82, 054121 (2010)
92. Li Yang, "First-principles study of the optical absorption spectra of electrically gated bilayer graphene," Phys. Rev. B 81, 155445 (2010)
93. David A. Siegel, Cheol-Hwan Park, C. Hwang, Jack Deslippe, A. V. Federov, Steven G. Louie, and Alessandra Lanzara, "Many-body Interactions in Quasi-freestanding Graphene," Proc. Natl. Acad. Sci. U.S.A. 108, 11365 (2011)
94. H. C. Hsueh, G. Y. Guo, and Steven G. Louie, "Excitonic Effects in the Optical Properties of a SiC Sheet and Nanotubes," Phys. Rev. B 84, 85404 (2011)
95. Georgy Samsonidze, Manish Jain, Jack Deslippe, Marvin L. Cohen, and Steven G. Louie, "Simple approximate physical orbitals for GW quasiparticle calculations," Phys. Rev. Lett. 107, 186404 (2011)
96. Georgy Samsonidze, Marvin L. Cohen, and Steven G. Louie, "Compensation-doped silicon for photovoltaic applications," Phys. Rev. B 84, 195201 (2011)
97. Manish Jain, James R. Chelikowsky, and Steven G. Louie, "Quasiparticle Excitations and Charge Transition Levels of Oxygen Vacancies in Hafnia," Phys. Rev. Lett. 107, 216803 (2011)
98. Manish Jain, James R. Chelikowsky, and Steven G. Louie, "Reliability of Hybrid Functionals in Predicting Band Gaps," Phys. Rev. Lett. 107, 216806 (2011)
99. Isaac Tamblyn, Pierre Darancet, Su Ying Quek, Stanimir A. Bonev, and Jeffrey B. Neaton, "Electronic energy level alignment at metal-molecule interfaces with a GW approach," Phys. Rev. B 84, 201402(R) (2011)
100. Li Yang, "Excitons in intrinsic and bilayer graphene," Phys Rev. B 83, 085405 (2011)
101. Li Yang, "Excitonic Effects on Optical Absorption Spectra of Doped Graphene," Nano Lett. 11, 3844 (2011)
102. Oleg V. Yazyev, Emmanouil Kioupakis, Joel E. Moore, and Steven G. Louie, "Quasiparticle effects in the bulk and surface-state bands of Bi2Se3 and Bi2Te3 topological insulators," Phys. Rev. B 85, 161101(R) (2012)
103. Sahar Sharifzadeh, Ariel Biller, Leeor Kronik, and Jeffrey B. Neaton, "Quasiparticle and Optical Spectroscopy of Organic Semiconductors Pentacene and PTCDA from First Principles," Phys. Rev. B 85, 125307 (2012)
104. Jesse Noffsinger, Emmanouil Kioupakis, Chris G. Van de Walle, Steven G. Louie, and Marvin L. Cohen, "Phonon-Assisted Optical Absorption in Silicon from First Principles," Phys. Rev. Lett. 108, 167402 (2012)
105. Cheol-Hwan Park, Feliciano Giustino, Catalin D. Spataru, Marvin L. Cohen, and Steven G. Louie, "Inelastic Carrier Lifetime in Bilayer Graphene," Appl. Phys. Lett. 100, 032106 (2012)
106. Kaihui Liu, Jack Deslippe, Fajun Xiao, Rodrigo B. Capaz, Xiaoping Hong, Shaul Aloni, Alex Zettl, Wenlong Wang, Xuedong Bai, Steven G. Louie, Enge Wang, Feng Wang, "A Periodic Table of Carbon Nanotube Optical Transitions". Nature Nanotechnology, 7:325--329 (2012)
107. Sangkook Choi, Jack Deslippe, R.B. Capaz, & S.G. Louie, "An explicit formula for optical oscillator strength of excitons in semiconducting single-walled carbon nanotubes: family behavior." Nano letters, 13(1), 54-58 (2012).
108. Sahar Sharifzadeh, Isaac Tamblyn, Peter Doak, Pierre Darancet, and Jeffrey B. Neaton, "Quantitative Molecular Orbital Energies within a G0W0 Approximation", Eur. Phys. J. B 85, 323 (2012)
109. Jack Deslippe, Georgy Samsonidze, Manish Jain, Cohen, M. L., and S.G. Louie. "Coulomb-hole summations and energies for GW calculations with limited number of empty orbitals: A modified static remainder approach." Physical Review B, 87(16), 165124. (2013)
110. Brad D. Malone and Marvin L. Cohen, "Quasiparticle semiconductor band structures including spin-orbit interactions," J. Phys.: Condens. Matter 25, 105503 (2013)
111. Georgy Samsonidze, Marvin L. Cohen, and Steven G. Louie, "First-principles study of quasiparticle energies of a bipolar molecule in a scanning tunneling microscope measurement," Comput. Mater. Sci. 91, 187 (2014)

# Information about how to set the various options here.
# Ideally you can use a file already created for your platform in this directory.
# Otherwise, you can work from the one most similar that is here.

# Select the Fortran compiler you are using.
# if you have a different one than these, modifications in Common/compiler.h
# and Common/common-rules.mk will be necessary.
COMPFLAG  = -D{INTEL, PGI, GNU, PATH, XLF, G95, ABSOFT, NAG, OPEN64, SUN, CRAY}

# Use -DMPI to compile Fortran in parallel with MPI. Otherwise is serial.
# Add -DOMP to compile with OpenMP support. Also add appropriate compiler-dependent flag to F90free:
# ifort, sunf90, absoft, pathscale, Open64: -openmp. PGI: -mp=nonuma. gfortran: -fopenmp. XLF: -qsmp=omp.
# crayftn: on by default (to turn off use -h noomp). g95 and NAG do not support OpenMP.
PARAFLAG  = -DMPI
# -DUSESCALAPACK enables usage of ScaLAPACK (required in parallel for BSE).
# -DUSEESSL uses ESSL instead of LAPACK in some parts of the code.
# -DUNPACKED uses unpacked rather than packed representation of the Hamiltonian
# in EPM. Packed LAPACK operations give bad results eventually in Si-EPM kernel 'max x'
# test for ACML, Cray LibSci, and MKL sometimes.
# -DFFTW3 uses fftw3 instead of fftw2, which is recommended for better performance, and enables threading.
# -DHDF5 enables usage of HDF5 for writing epsmat and bsemat files. The produced files will be
# eps0mat.h5, epsmat.h5 and bsemat.h5 and are used in place of eps0mat, epsmat, bsedmat, bsexmat
# (the latter two are combined in one .h5 file).
# Using -DHDF5 gives you substantially better IO performance in many cases by taking advantage
# of HDF5's parallel IO options and other options. However, you must have the HDF5 libraries
# installed on your system and define HDF5LIB and HDF5INCLUDE below.
MATHFLAG  = -DUSESCALAPACK -DUSEESSL -DUNPACKED -DHDF5
# For Fortran and C++. -DDEBUG enables extra checking. -DVERBOSE writes extra information.
# Only use these flags if you need to develop or debug BerkeleyGW.
# The output will be much more verbose, and the code will slow down by ~20%.
DEBUGFLAG = -DDEBUG -DVERBOSE
# Same, but for C.
C_DEBUGFLAG = -DDEBUG -DVERBOSE

# Command for the preprocessor. -ansi should generally be used.
# add -P if the Fortran compiler will not accept indication of line numbers.
# Use gcc's (often in /lib/cpp) or a C compiler (even mpicc) with "-E". Some need "-x c" as well.
FCPP    = cpp -ansi
# Fortran compiler and its flags for F90 and f90 files (free source form)
# see above at PARAFLAG regarding flags for OpenMP.
# With -DOMP and openmp flags here, you will get threaded BerkeleyGW.
# Without -DOMP, but with openmp flags here, is appropriate for just using threaded libraries.
# Sometimes, flags such as -fno-second-underscore or -assume 2underscores may be necessary
# to make linking succeed against C libraries such as FFTW, depending on what compiler built them.
F90free = {mpif90, mpiifort, ftn, ifort, pgf90, gfortran, ...}
# Fortran compiler and any flag(s) required for linking
LINK    = {mpif90, mpiifort, ftn, ifort, pgf90, gfortran, ...}
# Fortran optimization flags. The levels below will generally work.
FOPTS   = {-fast, -O3}
# Fortran optimization flags for epsilon_main and sigma_main which can have
# trouble in high optimization due to their long length. If below does not
# work, try -O2.
FNOOPTS = $(FOPTS) # Fortran compiler flag to specify location where module should be created. # different for each compiler, refer to examples. MOD_OPT = # Fortran compiler flag to specify where to look for modules. INCFLAG = -I # Use this to compile C++ in parallel with MPI. Leave blank for serial. # MPICH, MVAPICH, Intel MPI require also -DMPICH_IGNORE_CXX_SEEK, or an error may occur such as: # "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h" C_PARAFLAG = -DPARA # C++ compiling command and any needed flags CC_COMP = {mpiCC, mpicxx, mpiicpc, CC, icpc, pgCC, g++, ...} # C compiling command and any needed flags C_COMP = {mpicc, mpiicc, cc, icc, pgcc, gcc, ...} # C/C++ link command and any needed flags C_LINK = {mpiCC, mpicxx, mpiicpc, CC, icpc, pgCC, g++, ...} # C/C++ optimization flags C_OPTS = -fast # Note: for Intel compilers, it is equivalent to use icc or icpc on C++ files. # command to remove, for make clean REMOVE = /bin/rm -f # command for making archives (.a). Default is /usr/bin/ar. # Usually that is fine and AR does not need to be specified, but # to do interprocedural optimizations (IPO) with ifort, you need xiar instead. #AR = /usr/bin/env xiar # Math Libraries # path for FFTW library, used in lines below FFTWPATH = # link line for FFTW2 library. Sometimes needs to be -ldfftw FFTWLIB = -L$(FFTWPATH)/lib -lfftw
# link line for FFTW3 library, if -DFFTW3 is used. Including fftw_omp allows threaded run.
FFTWLIB      = -L$(FFTWPATH)/lib {-lfftw3_omp} -lfftw3 # FFTW2 requires include file fftw_f77.i; # Sometimes supercomputer installations will not have it. # If not, find it online and copy it: e.g. http://www.fifi.org/doc/fftw-dev/fortran/fftw_f77.i # FFTW3 requires include file fftw3.f03 instead. FFTWINCLUDE =$(FFTWPATH)/include

# Different styles will apply depending on the package used.
# Must provide BLAS as well as LAPACK: some packages will do this in one library file,
# others will not. See examples in this directory for how to link with MKL, ACML,
# ATLAS, Ubuntu packages, etc. For MKL, if you will use ScaLAPACK, it is most
# convenient to include BLACS here too. For further info on linking with MKL, see
LAPACKLIB    =

# Specify below if you have -DUSESCALAPACK in MATHFLAG.
# BLACS must be provided here too, if it is not provided in LAPACKLIB above. See
# examples in this directory for different packages, as with LAPACKLIB. Note that
# you may have problems if ScaLAPACK was not built with the same LAPACK used above.
SCALAPACKLIB =

# Specify below if you have -DHDF5 in MATHFLAG.
# If compiling in parallel, you must have HDF5 compiled with parallel support or linking will fail.
# Path as below should generally work. Sometimes -lsz too, or static linkage, might be required.
# Note that "-lz" is not from HDF5, but its dependency zlib.
HDF5PATH     =
HDF5INCLUDE  = $(HDF5PATH)/include HDF5LIB = -L$(HDF5PATH)/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lz

# Flags for performance profiling with an external tool such as IPM on NERSC
PERFORMANCE  =

# Command to submit testsuite job script from testsuite directory.
# qsub is for PBS. If no scheduler, put make check-parallel here.
# In serial, delete this line.
TESTSCRIPT = qsub {architecture}.scr


BerkeleyGW testsuite
David Strubbe 2009-2011

== Running tests ==

* To run the testsuite in serial, type "make check" in this directory or the main directory. "make check-save" will do the same, but retain the working directories for debugging.
* To run in parallel without a scheduler, you can just use "make check-parallel" if you do not have a scheduler (e.g. PBS). Set environment variable SAVETESTDIRS=yes to save working directories. The tests use 4 cores, so be sure that at least that many are available, or use BGW_TEST_MPI_NPROCS (see below).
* To run in parallel with a scheduler, type "make check-jobscript" or "make check-jobscript-save", which will execute the job script for the machine you are using, as specified in arch.mk by the line TESTSCRIPT. See example job scripts for various machines in this directory called *.scr. The tests use 4 cores, so be sure to request at least that many in the job script, or use BGW_TEST_MPI_NPROCS (see below).
* Environment variables:
- TEMPDIRPATH: sets the scratch directory where temporary working directories will be created. Default is /tmp, but on some machines you may not have permission to write there.
- MPIEXEC: sets the command for parallel runs. Default is which mpiexec. Note that mpiexec and mpirun are generally equivalent (except for Intel MPI, in which case mpirun is recommended). Set this if you are using a different command such as 'ibrun' (SGE parallel environment), 'runjob' (BlueGene), or 'aprun' (Cray), if you need to use a different mpiexec than the one in your path, or if some options need to be appended to the command. Depending on the value of this variable, three styles of command line are used: ibrun, runjob, and mpirun/aprun.
- BGW_TEST_MPI_NPROCS: set to overrule the number of processors listed in the test files. Useful for testing correctness of parallelization, if you don't have 4 cores, or to run the testsuite faster with more cores.
[- BGW_TEST_NPROCS: deprecated, same as BGW_TEST_MPI_NPROCS, provided for compatibility with versions 1.0.x.]
- MACHINELIST: if set, will be added to command line for MPI runs. This is needed in some MPI implementations.
- EXEC: if set, will be added before name of executable. Used to run code through valgrind.
* To run just one test, in its directory, run "../run_regression_test.pl [-s] [-p] -D ../../bin -f [testname].test". Include the -s flag to run in serial; otherwise it will be in parallel. Include the -p flag to preserve the working directory.

Contents:
(1) run_testsuite.sh -- this script runs tests from filenames ending in *.test in this directory.
(2) run_regression_test.pl -- called from run_testsuite.sh for each individual test.
(3) *.scr -- job scripts for running the testsuite on various parallel machines.
(4) interactive*.sh -- scripts to run in parallel, in interactive mode. You have to follow the instructions in the script, not just run it.
(5) queue_monitor.pl -- a Perl script for parallel tests with a SLURM or PBS scheduler, which submits a job and monitors the queue to see what happens. Used by the BuildBot.
(6) test directories.
(7) fix_testsuite.py -- (for developers) can be used to create or update match reference values in test files.
(8) no_hires.sh -- Some clusters will not have the Perl package Time::HiRes installed which is needed for timing in run_regression_test.pl. You can just deactivate the usage with this script.
(9) buildbot_query.pl -- (for developers) can be used to find the range of values obtained on the buildslaves for a particular match, to set values in the test files.

== Writing tests ==

The test files consist of lines beginning with one of a set of tags, parsed by the Perl script. Comment lines beginning with '#' will be ignored.
Test : title
Write a title to output to identify the test. Should be the first tag in the file.
Banner : text
Write a heading in a box to identify a specific part of a test. Helpful when input files are generated by sed and do not have a distinct name.
Enabled : Yes/No
If Yes, will be run; if No, will not be run. Use to turn off a test without deleting it from the repository. Should be the second tag in the file.
TestGroups : group-name [group-name2 [...]]
The run_testsuite.sh script can be run with argument "-g" and a list of groups. Then tests will only be run if there is a match between the argument list and the list in TestGroups. Examples of groups that could be used: parallel, serial, long. [This tag is actually read by run_testsuite.sh rather than run_regression_test.pl.]
Executable : program.x
Name of executable to be run (path is bin directory). Persists for multiple runs, until next Executable tag.
Processors : integer
Number of processors to use. Ignored if mpiexec is not available. May not exceed the number in the reservation in the job scripts.
Set to special value "serial" to run without mpiexec.
Command : shell-command
Specify a shell command, which will be executed in the working directory. Useful for renaming log files that would be overwritten by a subsequent run, or preprocessing input files by sed or other utilities (after putting in working directory with Copy).
Copy : file.in [file_newname.in]
Copy a file from test directory to run directory. If new name is not supplied, original name will be used. Useful if you want to sed a file before it is run.
Unpack : data.tar.gz
The file data.tar.gz in the test directory will have "tar xzf" run on it, with resulting files going to the working directory.
Output : file.out
Output will be piped into the file named here, in the working directory.
Arguments : arg1 arg2
The current Executable will be executed (in serial) with the text given here as command-line argument(s). No files will be copied to working directory. Use redirection with ">" to capture the output if necessary.
Input : file.in [file_newname.in/PIPE/CMDLINE/NONE]
The file named here will be copied from the test directory to the working directory, for use as input. If it is followed by "PIPE", the file will be piped into the executable. If it is followed by "CMDLINE", the file will be given as a command-line argument to the executable. If it is followed by "NONE", no file will be copied (useful if an input file was already generated by sed in the working directory). If it is followed by another name, the file's name in the working directory will be the new name. This tag causes actual execution of the run that has been set up by previous tags.
Precision : 1e-5
A floating point number, the tolerance for testing whether a match has passed or failed. Persists until next Precision tag. Default is 1e-4.
match ; name ; COMMAND(..); reference-value
Extracts a calculated number from a run and tests it against the reference value. The name is an identifier printed to output. The number is extracted as the standard output from the listed COMMAND, which is one of this set:
. GREP(filename, 'search-text', field, offset)
Finds the first line in file containing 'search-text' (which MAY NOT contain a comma), and returns the specified field of that line. "Field" is meant in the sense used by 'awk', i.e. the line is parsed into white-space separated groups, indexed starting with 1. The optional 'offset' directs the use of the Mth line after the line containing 'search-text'.  No offset is equivalent to offset = 0. This is the most robust of the commands and should be used when possible in preference to the others.
. SIZE(filename)
Returns the size of the specified file via 'ls -lt'. Useful for binary files whose contents cannot easily be checked.
. LINE(filename, line, field)
Returns the specified field of the specified line number from the file. Use GREP instead if possible.
. SHELL(shell-command)
The result is the standard output of the listed command. Deprecated; use GREP or LINE unless absolutely necessary.
STOP TEST
For debugging purposes, to halt test after the part you are studying has run.


-----------------------------------------------------------------
----------  BerkeleyGW library  ---------------------------------
-----------------------------------------------------------------

To build other codes with BerkeleyGW output support, type 'make library'
to create libBGW_wfn.a and wfn_rho_vxc_io_m.mod (and dependent modules),
and then compile with -I library/ and link library/libBGW_wfn.a with
the other code.

An m4 macro for configure scripts is provided in this directory, for
use in linking to this library. Codes linking the library should 'use'
the module 'wfn_rho_vxc_io_m'.

To generate real wavefunctions, a Gram-Schmidt process should be used.
The appropriate parallelization scheme etc. will be dependent on the code,
and cannot be easily handled in a general manner here, but examples can
be found in MeanField/SIESTA/real.f90 and MeanField/ESPRESSO/pw2bgw.f90
(routine real_wfng).


Brief descriptions of the scripts in this directory:

----Energies-----

qp_shifts.py - from sigma_hp.log file, writes two files which contain the LDA
energies and the GW shifts (E_qp-E_lda) for that energy. Useful
for determining scissor shifting parameters ecdel, evdel, etc.

eqp.py       - extracts QP energies from sigma_hp.log file and generates file
eqp.dat. This file can be read in directly from the BGW
code if you want to shift the energies for each kpoint and band
exactly instead of relying on the scissor shift.

----Kpoints-----

kptlist.pl   - extracts a formatted list of k-points from PARATEC file for use in the Sigma code

qptlist.pl   - extracts a formatted list of q-points from PARATEC file for use in the Epsilon code



All the DFT examples may be done with either ESPRESSO or PARATEC.
Each directory's README tells you how to run it and suggests number of processors and walltime for parallel calculations.
Needed pseudopotentials and some useful scripts for them are contained in DFT/pseudos.

Note: ESPRESSO examples are compatible with Quantum ESPRESSO 5.0 and later versions.
If you want to run them with Quantum ESPRESSO 4.3.2 or earlier version, you should modify the input files for pw.x.
Change "calculation = 'bands'" to "calculation = 'nscf'" and "CELL_PARAMETERS" to "CELL_PARAMETERS cubic".

This directory contains example runs for a variety of physical systems:

silicon: a bulk semiconductor
Includes PREBUILT tarball of DFT inputs from PARATEC.
Includes ref directories containing sample output from ESPRESSO and BerkeleyGW steps.
Available for EPM as well as DFT.
Shows how to use Wannier90 and sig2wan.x to obtain a GW bandstructure by interpolation.

Si2_bs: another silicon example
Shows how to use inteqp to obtain a GW bandstructure by interpolation.

Si2_sapo: another silicon example
Shows how to perform iterative Davidson diagonalization in SAPO.
It requires pw2bgw with Vsc capability as in espresso-5.0.2

sodium: a bulk metal

swcnt_5-5: (5,5) single-walled carbon nanotube, a metallic 1D system

swcnt_8-0: (8,0) single-walled carbon nanotube, a semiconducting 1D system
Has runs of plotxct with visualization by volume.py and surface.x.

CO: a small molecule

benzene: a slightly larger molecule
Includes run of gsphere.py and SIESTA.

There are also examples in the Visual directory for the scripts there.
The testsuite runs may also be consulted, although they are not realistic calculations.


## MeanField

-----------------------------------------------------------------
----------  MeanField -------------------------------------------
-----------------------------------------------------------------

Description:

BerkeleyGW uses a mean-field starting point, typically from DFT.
Currently, BerkeleyGW supports two plane-wave DFT codes,
PARATEC and Quantum ESPRESSO; one localized-orbital DFT code, SIESTA;
and two real-space codes, Octopus and PARSEC.
You can find details on how to use BerkeleyGW with these codes in
their respective directories.

For testing purposes and for crude calculations of large systems,
BerkeleyGW can be executed on top of the empirical pseudopotential
plane-wave code. See MeanField/EPM for details.

There is a tool for generating large numbers of unoccupied orbitals
(approximate from plane waves or exact by iterative diagonalization).
It is located in MeanField/SAPO.

You can find a simple code for computing the Coulomb integral within
an image-charge model in MeanField/ICM.

-----------------------------------------------------------------

Tricks and hints:

1. Vxc0

Vxc0 is the G=0 component of the exchange-correlation potential Vxc.
Vxc0 is added to the eigenvalues in the wavefunction files produced
by PARATEC and ESPRESSO. Vxc0 is also included in the VXC and vxc.dat
files produced by PARATEC and ESPRESSO (the VXC file contains Vxc(G)
and the vxc.dat file contains matrix elements of Vxc). The two Vxc0
terms cancel out when calculating the quasiparticle corrections
in the Sigma code.

2. Vacuum level

To correct the DFT eigenvalues for the vacuum level take the average
of the electrostatic potential on the faces of the unit cell in the
non-periodic directions and subtract it from the DFT eigenvalues.
The electrostatic potential is defined as Velec = Vbare + Vhartree,
while the total potential is Vtot = Vbare + Vhartree + Vxc, hence
Vtot contains Vxc0 and Velec does not. The average of Velec is
fed into the Sigma code using keywords avgpot and avgpot_outer.
The potentials can be generated with PARATEC and ESPRESSO.
In PARATEC, use elecplot for Velec or potplot for Vtot, then
convert from a3dr to cube using the Visual/volume.py script.
In ESPRESSO, use iflag=3, output_format=6, and plot_num=11
for Velec or plot_num=1 for Vtot. The averaging is done with
the Visual/average.py script.

3. Unit cell size

If you truncate the Coulomb interaction, make sure that the size
of the unit cell in non-periodic directions is at least two times
larger than the size of the charge distribution. This is needed
to avoid spurious interactions between periodic replicas but at
the same time not to alter interactions within the same unit cell.
Run Visual/surface.x to plot an isosurface that contains 99% of the
charge density (see Visual/README for instructions on how to do this).
The code will print the size of the box that contains the isosurface
to stdout. Multiply the box dimensions in non-periodic directions
by two to get the minimum size of the unit cell.

4. Inversion symmetry

When using the real flavor of the code, make sure the inversion
symmetry has no associated fractional translation (if it does,
shift the coordinate origin). Otherwise WFN, VXC, RHO (and VSC
in SAPO) have non-vanishing imaginary parts which are simply
dropped in the real flavor of the code. This won't do any



## ESPRESSO

Quantum ESPRESSO is available for download at http://www.quantum-espresso.org/

The interface between Quantum ESPRESSO and BerkeleyGW consists of three programs,
kgrid.x, pw2bgw.x and bgw2pw.x. kgrid.x is compiled with BerkeleyGW package and
pw2bgw.x and bgw2pw.x are compiled with Quantum ESPRESSO.
Files for versions 4.3.2, 5.0.x, and 5.1.x are supplied here.
Starting with version 5.0, compatible files of pw2bgw.f90 and bgw2pw.f90 are
distributed with Quantum ESPRESSO.

The development versions of pw2bgw.f90 and bgw2pw.f90 are available from
Quantum ESPRESSO trunk. Quantum ESPRESSO allows anonymous checkouts of its
source code. Use the command below and use 'anonymous' as the username and
a blank password to checkout the code:
svn checkout http://qeforge.qe-forge.org/svn/q-e/trunk/espresso

You can find more details about Quantum ESPRESSO svn on this website:
http://www.qe-forge.org/gf/project/q-e/scmsvn/

--------------------------------------------------------------------------------

kgrid.x

pw.x can automatically generate a uniform grid of k-points, either unshifted
or shifted by half a grid step (Monkhorst-Pack grid), and reduce it to the
irreducible wedge of the Brillouin Zone with the symmetries of the point group
of the Bravais lattice and optionally with time-reversal symmetry. The same
functionality (and more) is provided by kgrid.x in this directory. Additionally,
kgrid.x can use the symmetries of the space group of the crystal instead of the
symmetries of the point group of Bravais lattice, which is needed for BerkeleyGW.
kgrid.x is not limited to the unshifted/half-step shifted Monkhorst-Pack grids.
It can generate an asymmetrically shifted fine grid used to improve the
convergence in absorption calculations. Also, kgrid.x can generate a grid
of k-points with a small q-shift used in Epsilon calculation to avoid the
divergence of the Coulomb interaction. The list of k-points generated by
kgrid.x must be manually added to the input file of pw.x. Note that time-reversal
symmetry should NOT be used for BerkeleyGW (noinv = .false. if generating the
k-grid in pw.x).

The format of the input file for kgrid.x (along with an example for Si) is found
the input files for kgrid.x in examples/DFT in the ESPRESSO subdirectories of
each example.

--------------------------------------------------------------------------------

pw2bgw.x

Converts the output files produced by pw.x to the input files for BerkeleyGW.

You cannot use USPP, PAW, or spinors in a pw.x run for BerkeleyGW.

You cannot use "K_POINTS gamma" in a pw.x run for BerkeleyGW.
Use "K_POINTS { tpiba | automatic | crystal }" even for the
Gamma-point calculation.

The format of the input file for pw2bgw.x is described
in files MeanField/ESPRESSO/version-4.3.2/pw2bgw.inp,
MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.html (copy of espresso-5.1/PP/Doc/INPUT_pw2bgw.html),
which is generated from MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.def, and
MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.html (copy of espresso-5.0.3/PP/Doc/INPUT_pw2bgw.html),
which is generated from MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.def.
You can find the input files for pw2bgw.x in examples/DFT
in the ESPRESSO subdirectories of each example.

Version 4.3.2 and earlier:

It is recommended to run a pw.x "nscf" calculation with "K_POINTS crystal"
and a list of k-points produced by kgrid.x.

Sometimes pw.x generates additional k-points in a "nscf" run with an explicit
list of k-points. If this is the case for your calculation, there are several
ways to go around this problem:

* Apply the patch provided with BerkeleyGW. It will prevent pw.x from
generating additional k-points if they are provided explicitly, and
take care of the normalization of the weights of k-points in a "bands"
calculation.
* Do not specify the atomic positions in the input file of kgrid.x (set
number of atoms = 0). Then pw.x will generate additional k-points which
are the correct ones. Also set noinv = .true. in the input file of pw.x
if time-reversal symmetry was not used in kgrid.x.
* Run a pw.x "bands" calculation instead of "nscf". In this case you have
to explicitly specify the occupations in the input file of pw2bgw.x (note
that this only works for insulators) and to normalize the weights of
k-points to one in the input file of pw.x.

Version 5.0 and later:

It is recommended to run a pw.x "bands" calculation with "K_POINTS crystal"
and a list of k-points produced by kgrid.x.

You can also run a pw.x "nscf" calculation instead of "bands", but in this
case pw.x may generate more k-points than provided in the input file of pw.x.
If this is the case for your calculation you will get errors in BerkeleyGW.

--------------------------------------------------------------------------------

bgw2pw.x

Converts BerkeleyGW WFN and RHO files to the format of pw.x.
This can be useful, for example, if you generate the plane waves
on top of the valence bands and want to diagonalize them in pw.x.
Look at the documentation for SAPO code in BerkeleyGW for more information.
Another possible use is to convert between different versions of pw.x.

bgw2pw.x reads common parameters from file prefix.save/data-file.xml and
writes files prefix.save/charge-density.dat (charge density in R-space),
prefix.save/gvectors.dat (G-vectors for charge density and potential),
prefix.save/K$n/eigenval.xml (eigenvalues and occupations for nth k-point), prefix.save/K$n/evc.dat (wavefunctions in G-space for nth k-point), and
prefix.save/K$n/gkvectors.dat (G-vectors for nth k-point). You must have prefix.save/K$n/eigenval.xml files present, or an error will occur,
even though their contents will not be used and will be overwritten.
The best is to run a pw.x calculation and use its prefix.save, e.g. from scf
and then get unoccupied bands from bgw2pw.x.

bgw2pw.x doesn't create restart files, so you cannot use restart_mode = 'restart'
for a subsequent pw.x run. Instead, use startingwfc = 'file'. Make sure
wf_collect = .true. and there are no prefix.wfc* files present. Also, the pw.x run
that generated the prefix.save directory originally must have wf_collect = .true.
also, for the appropriate links to the K$n files to be present. bgw2pw.x doesn't modify file prefix.save/data-file.xml so make changes to this file manually. For example, you will need to change the NUMBER_OF_BANDS and NUMBER_OF_PROCESSORS tags (as well as per pool and per image) to make sure these match the number of bands from the WFN file, as well as the number of processors you will use in a subsequent run. The format of the input file for bgw2pw.x is described in files MeanField/ESPRESSO/version-4.3.2/bgw2pw.inp, MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.html (copy of espresso-5.1/PP/Doc/INPUT_bgw2pw.html), which is generated from MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.def, and MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.html (copy of espresso-5.0.3/PP/Doc/INPUT_bgw2pw.html), which is generated from MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.def. -------------------------------------------------------------------------------- Notes on running pw.x Sometimes pw.x crashes when trying to generate a LARGE number of unoccupied states needed for GW calculations. The error messages may refer to "Cholesky decomposition" or "diagonalization". If you run into this problem try one of the following workarounds, or a combination of them: 1) Increase ecutwfc. Iterative diagonalization becomes inefficient and unstable with increasing the ratio of the number of states to the size of the Hamiltonian. Increasing ecutwfc will decrease this ratio at the cost of computation time. 2) Split the calculation over k-points. If one k-point fails, it won't affect the other k-points. You can merge the final wavefunction file using MeanField/Utilities/wfnmerge.x after running pw2bgw.x for each k-point. 3) Start with random instead of randomized atomic wavefunctions. For this use the following parameter in the input file of pw.x: startingwfc = 'random' 4) Split the diagonalization into several steps alternating between different diagonalization schemes. For example, use the following parameters in the input files for consequent runs of pw.x: 1st run: conv_thr = 1.0d-2 diagonalization = 'david' 2nd run: conv_thr = 1.0d-4 diagonalization = 'cg' startingwfc = 'file' 3rd run: conv_thr = 1.0d-6 diagonalization = 'david' startingwfc = 'file' etc. 5) Run pw.x with "-ndiag 1". Often serial diagonalization is more stable than the parallel one, and the time and memory overhead is bearable in most cases. 6) Compile pw.x without "-D__SCALAPACK" in DFLAGS in make.sys for using a custom distributed-memory diagonalization instead of ScaLAPACK. This is useful to check if the problem is caused by improper installation of ScaLAPACK. Note that you will have to explicitly specify ndiag, e.g. "mpirun -np 24 pw.x -ndiag 16 -in prefix.in > prefix.out", because pw.x only sets ndiag automatically in case of ScaLAPACK. Finally, it is recommended to always use the following parameters in the input files for pw.x: wf_collect = .true. diago_full_acc = .true. See documentation on Quantum ESPRESSO for information on these parameters. BEWARE: Sometimes wavefunctions may lose orthogonality during iterative diagonalization. Neither Quantum ESPRESSO nor BerkeleyGW checks for orthogonality of wavefunctions. This may cause erroneous behavior like diverging head of eps0mat and possibly many other things.  ## MeanField/ESPRESSO/kgrid.inp 5 5 5 ! numbers of k-points along b1,b2,b3 0.5 0.5 0.5 ! k-grid offset (0.0 unshifted, 0.5 shifted by half a grid step) 0.0 0.0 0.001 ! a small q-shift (0.0 unshifted, 0.001 shifted by one 1000th of b3) 0.0 0.5 0.5 ! lattice vectors in Cartesian coordinates (x,y,z) 0.5 0.0 0.5 ! in units of the lattice parameter 0.5 0.5 0.0 ! 2 ! number of atoms in the unit cell 1 -0.125 -0.125 -0.125 ! atomic species and positions in Cartesian coordinates (x,y,z) 1 0.125 0.125 0.125 ! in units of the lattice parameter 0 0 0 ! size of FFT grid .false. ! use time-reversal symmetry. Set to false for BerkeleyGW .false. ! OPTIONAL: k-points in the log file are in Cartesian coordinates .false. ! OPTIONAL: output is in Octopus format # Above: typical values for Si. Below: general description. # nk1 nk2 nk3 ! numbers of k-points in crystal coordinates (b1,b2,b3) # dk1 dk2 dk3 ! k-grid offset (0.0 unshifted, 1.0 shifted by bj/nkj) # dq1 dq2 dq3 ! a small q-shift (0.0 unshifted, 1.0 shifted by bj) # a1x a1y a1z ! lattice vectors in Cartesian coordinates (x,y,z) # a2x a2y a2z ! in arbitrary units (bohr, angstrom, lattice parameter) # a3x a3y a3z ! # n ! number of atoms in the unit cell # s1 x1 y1 z1 ! atomic species and positions in Cartesian coordinates (x,y,z) # ........... ! in the same units as the lattice vectors # sn xn yn zn ! # nr1 nr2 nr3 ! size of FFT grid # trs ! if set to .true., use time-reversal symmetry (do not use this for BerkeleyGW) # Cartesian ! OPTIONAL: set to .true. for k-points in Cartesian coordinates (only in the log file) # octopus ! OPTIONAL: set to .true. to write output file in format suitable for Octopus  ## MeanField/ESPRESSO/version-5.1/INPUT_pw2bgw.html This file has been created by helpdoc utility. ## MeanField/ESPRESSO/version-5.1/INPUT_bgw2pw.html This file has been created by helpdoc utility. ## MeanField/ESPRESSO/version-5.0/INPUT_pw2bgw.html This file has been created by helpdoc utility. ## MeanField/ESPRESSO/version-5.0/INPUT_bgw2pw.html This file has been created by helpdoc utility. ## MeanField/ESPRESSO/version-4.3.2/pw2bgw.inp &input_pw2bgw prefix = 'silicon' ! same as in espresso real_or_complex = 1 ! 1 for real or 2 for complex wfng_flag = .true. ! write wavefunction in G-space wfng_file = 'WFN' ! wavefunction file name wfng_kgrid = .false. ! overwrite k-grid in wavefunction file wfng_nk1 = 4 ! ( if espresso input file contains the wfng_nk2 = 4 ! manual list of k-points, the k-grid wfng_nk3 = 4 ! parameters in espresso are set to zero; wfng_dk1 = 0.5 ! since Sigma and absorption both need to know wfng_dk2 = 0.5 ! the k-grid dimensions, we patch these wfng_dk3 = 0.5 ! parameters into the wave-function file ) wfng_occupation = .true. ! overwrite occupations in wavefunction file wfng_nvmin = 1 ! ( set min/max valence band indices; identical to wfng_nvmax = 4 ! scissors operator for LDA-metal/GW-insulator ) rhog_flag = .true. ! write charge density in G-space rhog_file = 'RHO' ! charge density file name vxcg_flag = .true. ! write exchange-correlation potential in G-space vxcg_file = 'VXC' ! exchange-correlation potential file name vxc0_flag = .true. ! write Vxc(G=0) vxc0_file = 'vxc0.dat' ! Vxc(G=0) file name vxc_flag = .false. ! write matrix elements of Vxc vxc_file = 'vxc.dat' ! Vxc matrix elements file name vxc_integral = 'g' ! compute Vxc matrix elements in R- or G-space vxc_diag_nmin = 0 ! min band index for diagonal Vxc matrix elements vxc_diag_nmax = 0 ! max band index for diagonal Vxc matrix elements vxc_offdiag_nmin = 0 ! min band index for off-diagonal Vxc matrix elements vxc_offdiag_nmax = 0 ! max band index for off-diagonal Vxc matrix elements input_dft = 'sla+pz' ! same as in espresso exx_flag = .false. ! set to .true. for hybrids vnlg_flag = .false. ! write Kleinman-Bylander projectors in G-space vnlg_file = 'KBproj' ! Kleinman-Bylander projectors file name vxc_zero_rho_core = .true. ! NLCC: remove core charge when calculating Vxc / # above are typical values for Si. below are the defaults. prefix = 'prefix' real_or_complex = 2 wfng_flag = .false. wfng_file = 'WFN' wfng_kgrid = .false. wfng_nk1 = 0 wfng_nk2 = 0 wfng_nk3 = 0 wfng_dk1 = 0.0 wfng_dk2 = 0.0 wfng_dk3 = 0.0 wfng_occupation = .false. wfng_nvmin = 0 wfng_nvmax = 0 rhog_flag = .false. rhog_file = 'RHO' vxcg_flag = .false. vxcg_file = 'VXC' vxc0_flag = .false. vxc0_file = 'vxc0.dat' vxc_flag = .false. vxc_file = 'vxc.dat' vxc_integral = 'g' vxc_diag_nmin = 0 vxc_diag_nmax = 0 vxc_offdiag_nmin = 0 vxc_offdiag_nmax = 0 input_dft = 'sla+pz' exx_flag = .false. vnlg_flag = .false. vnlg_file = 'VNL' vxc_zero_rho_core = .true.  ## MeanField/ESPRESSO/version-4.3.2/bgw2pw.inp &input_bgw2pw prefix = 'silicon' ! same as in espresso real_or_complex = 1 ! 1 for real or 2 for complex wfng_flag = .true. ! read wavefunction in G-space wfng_file = 'WFN' ! wavefunction file name wfng_nband = 0 ! number of bands to write (0 = all) rhog_flag = .true. ! read charge density in G-space rhog_file = 'RHO' ! charge density file name / # above are typical values for Si. below are the defaults. prefix = 'prefix' real_or_complex = 2 wfng_flag = .false. wfng_file = 'WFN' wfng_nband = 0 rhog_flag = .false. rhog_file = 'RHO'  ## MeanField/ESPRESSO/version-4.3.2/README_patch  This directory contains a patch for espresso-4.3.2 that fixes bugs listed below. Assuming BerkeleyGW is installed in$BGWPATH/BerkeleyGW,
to apply the patch execute the following command
in the directory containing the espresso-4.3.2 directory:

% patch -p0 -i $BGWPATH/BerkeleyGW/MeanField/ESPRESSO/version-4.3.2/espresso-4.3.2-patch espresso-4.3.2 buglist: (1) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> If you run espresso nscf calculation with startingwfc set to file you may get error message saying "cannot read wfc : file not found". This happens because subroutine verify_tmpdir in PW/input.f90 renames data-file.xml to data-file.xml.bck and subroutines read_planewaves and read_wavefunctions in PW/pw_restart.f90 try to read from data-file.xml which doesn't exist. To get around this problem read from .xml.bck in read_planewaves and read_wavefunctions if opening .xml returns error. (2) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Missing "CALL stop_pp ( )" at the end of PP/plan_avg.f90 causes it to crash sometimes. (3) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Sometimes pw.x generates additional k-points in a "nscf" run with an explicit list of k-points. If this is the case for your calculation, there are several ways to go around this problem: * Apply the patch provided with BerkeleyGW. It will prevent pw.x from generating additional k-points if they are provided explicitly, and take care of the normalization of the weights of k-points in a "bands" calculation. * Do not specify the atomic positions in the input file of kgrid.x (set number of atoms = 0). Then pw.x will generate additional k-points which are the correct ones. Also set noinv = .true. in the input file of pw.x if time-reversal symmetry was not used in kgrid.x. * Run a pw.x "bands" calculation instead of "nscf". In this case you have to explicitly specify the occupations in the input file of pw2bgw.x (note that this only works for insulators) and to normalize the weights of k-points to one in the input file of pw.x.  ## MeanField/ESPRESSO/patch_oldversions/README  This directory contains patches for older versions of espresso that fixes bugs listed below. Assuming BerkeleyGW is installed in$BGWPATH/BerkeleyGW,
to apply the patch execute the following command
in the directory containing the espresso-xxx directory:

% patch -p0 -i $BGWPATH/BerkeleyGW/MeanField/ESPRESSO/patch_oldversions/espresso-xxx-patch espresso buglist: (1) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> If you run espresso nscf calculation with startingwfc set to file you may get error message saying "cannot read wfc : file not found". This happens because subroutine verify_tmpdir in PW/input.f90 renames data-file.xml to data-file.xml.bck and subroutines read_planewaves and read_wavefunctions in PW/pw_restart.f90 try to read from data-file.xml which doesn't exist. To get around this problem read from .xml.bck in read_planewaves and read_wavefunctions if opening .xml returns error. (2) <<< THIS IS FIXED IN QUANTUM ESPRESSO 5.0 >>> Missing "CALL stop_pp ( )" at the end of PP/plan_avg.f90 causes it to crash sometimes.  ## PARATEC ## MeanField/PARATEC/README paratecSGL is available for download through SVN repository at https://civet.berkeley.edu/svn/CODES/paratecSGL/ (only for authorized users). To build with support for BerkeleyGW output, in arch.mk set the line GWWFNPATH to BerkeleyGW/library, and add -DBGW to M4OPTLIBS. Full documentation for PARATEC 5.1: http://www.tcm.phy.cam.ac.uk/~jry20/paratec/doc/doc.html Literature: * B. G. Pfrommer, J. Demmel, and H. Simon, "Unconstrained Energy Functionals for Electronic Structure Calculations," J. Comp. Phys. 150, 287 (1999). * B. G. Pfrommer, M. Cote, S. G. Louie, and M. L. Cohen, "Relaxation of Crystals with the Quasi-Newton Method," J. Comp. Phys. 131, 233 (1997). * Mathieu Taillefumier, Delphine Cabaret, Anne-Marie Flank, and Francesco Mauri, "X-ray absorption near-edge structure calculations with pseudopotentials: Application to the K-edge in diamond and alpha-quartz," Phys. Rev. B 66, 195107 (2002). * http://cmsn.drupalgardens.com/sites/cmsn.drupalgardens.com/files/CMSN_Newsletter_Vol2No2.pdf [An older version was available at http://www.nersc.gov/projects/paratec. PARATEC 5.1 produces only the old GW wavefunction format, incompatible with this version of BerkeleyGW. However, you can convert them to the new format using MeanField/Utilities/convert_old_to_new.x.] The pseudopotentials for PARATEC can be generated with the fhi98PP program which is available for download at http://www.fhi-berlin.mpg.de/th/fhi98md/fhi98PP/ PARATEC output for BerkeleyGW is controlled by flags gw_shift, gwc, gwr, gwscreening, gwcscreening, and vxc_matrix_elements. The flags can be combined with an underscore: e.g. output_flags gwr_gwscreening gwr and gwc are incompatible; gwscreening and gwcscreening are incompatible. gw_shift q1 q2 q3 -- generates q-shifted grid, q-vector is in crystal coordinates in units of reciprocal lattice vectors (for WFNq, WFNq_fi) This variable does the same job as the kgrid.x utility. output_flags gwc -- writes complex wavefunctions in G-space, for systems without inversion symmetry about the origin, to file WFN (for all codes). output_flags gwr -- writes real wavefunctions in G-space, for systems with inversion symmetry about the origin, to file WFN (for all codes) output_flags gwscreening -- writes charge density in G-space to file RHO, exchange-correlation potential in G-space to file VXC, and matrix elements of exchange-correlation potential to file vxc.dat (for Sigma). Real if possible and gwc not set, else complex. output_flags gwcscreening -- like gwscreening, except forces complex even if real is possible. vxc_matrix_elements diagmin diagmax offdiagmin offdiagmax -- specifies the range of bands for which to compute diagonal and off-diagonal matrix elements of exchange-correlation potential (for Sigma, in conjunction with output_flags gwscreening) Other key input flags: pw_job {scf, nonselfcon} -- Use scf for initial calculation, nonselfcon for generating BerkeleyGW outputs. (bandstructure does not seem to work) energy_cutoff ecut -- Plane-wave cutoff for wavefunctions, in Ry. number_kpoints -- set to 0 to use k_grid and reduce with symmetries set to -1 to use k_grid and do not reduce with symmetries set to any other number to read from file KPOINTS k_grid nx ny nz -- 3 integers specifying Monkhorst-Pack k-grid dimensions k_grid_shift dx dy dz -- Monkhorst-Pack k-grid shifts (typically 0.0 or 0.5) number_bands nb -- Number of bands to use in calculation. Fraction actually useful or written to BerkeleyGW output determined by next variable. eigspacefrac frac -- Fraction of bands to converge. Setting a higher number_bands and lower eigspacefrac can make the calculation more efficient depending on the diagonalization scheme. 0 < frac <= 1.0. You can find the actual input files for PARATEC and BerkeleyGW in examples/DFT, in PARATEC subdirectories for each example. There are also bgw2para and rho2cd utilities that convert BerkeleyGW files WFN and RHO to PARATEC format. This may be useful, for example, if one generates the plane waves on top of the valence and conduction bands (look into MeanField/SAPO/README for details) and wants to diagonalize them further in PARATEC. There are no input files; bgw2para takes as argument the wfn filename, and it creates files WFN$n.$s and BAND needed for PARATEC. Similarly, rho2cd requires file RHO and it creates file CD.  ## SIESTA ## MeanField/SIESTA/README An example siesta2bgw calculation is provided in examples/DFT/benzene. Please see this example for usage and example siesta and denchar input files. The SIESTA wrapper reads lattice vectors, atomic species and positions from SystemLabel.XV file, k-points from SystemLabel.KP file, eigenvalues from SystemLabel.EIG file, wavefunctions in R-space from SystemLabel{.K$k}.WF$n{.UP|.DOWN}{.REAL|.IMAG}.cube file, symmetry group, kinetic energy cutoffs for wavefunctions and charge density, k-grid dimensions and offsets from the input file, generates reciprocal lattice vectors, rotation matrices, fractional translations, FFT grid and G-vectors, performs FFT from R-space to G-space, and writes the selected range of bands to the output WFN file. Make sure to set up the real space grid in SIESTA/DENCHAR utility same as FFT grid. If the two grids differ the SIESTA wrapper will return an error. The output WFN file can be used as an auxiliary wavefunction for the SAPO code. A full GW/BSE calculation with SIESTA wavefunctions also requires RHO and VXC files. These files can be generated from SystemLabel.RHO{.UP|.DN}.cube, SystemLabel.VT{.UP|.DN}.cube and SystemLabel.VH.cube files obtained with SIESTA/GRID2CUBE utility on SIESTA real space grid. Make sure SIESTA real space grid is equivalent to FFT grid by setting parameter MeshCutoff in SIESTA input file same as kinetic energy cutoff for charge density. Input is read from file siesta2bgw.inp: &input_siesta2bgw systemlabel = 'ammonia' wfng_output_file = 'wfng.lo' rhog_output_file = '' vxcg_output_file = '' ecutwfn = 60.0 ecutrho = 240.0 wfng_nk1 = 1 wfng_nk2 = 1 wfng_nk3 = 1 wfng_dk1 = 0.0 wfng_dk2 = 0.0 wfng_dk3 = 0.0 wfng_ref_flag = .true. wfng_ref_kpoint = 1 wfng_ref_spin = 1 wfng_ref_band = 4 wfng_ref_energy = -5.87 wfng_band_flag = .true. wfng_band_min = 5 wfng_band_max = 28 wfng_energy_flag = .false. wfng_energy_min = 0.0 wfng_energy_max = 0.0 wfng_gamma_real = .true. / Here, lattice vectors, k-points, eigenvalues and wavefunctions in R-space are read from ammonia.XV, ammonia.KP, ammonia.EIG and ammonia.WF$n.cube
files, respectively. The kinetic-energy cutoffs for
wavefunction and charge density are set to 60 and 240 Ry, respectively.
The k-grid is set to the Gamma-point. The SIESTA eigenvalues are shifted
in energy so that the HOMO state (1st k-point, 1st spin, 4th band) appears
at -5.87 eV. The real parts of resonant SIESTA wavefunctions (from 5th to
28th band) are read from Gaussian Cube files and the imaginary parts are
set to zero (wfng_gamma_real), the wavefunctions are brought from R-space
to G-space and written to wfng.lo file. The SIESTA charge density and
exchange-correlation potential files are not generated.




This directory contains a patch for denchar-1.4 and
grid2cube-1.1.1 in siesta-3.1 that adds support
for non-orthogonal cells. The modified versions
generate Gaussian Cube files on real-space grid.
To apply the patch execute the following command
in the directory where you have siesta-3.1:

% patch -p0 -i siesta-3.1-patch

Use the following keywords in siesta input file:

WaveFuncKPointsScale ReciprocalLatticeVectors
%block WaveFuncKPoints
0.000  0.000  0.000
%endblock WaveFuncKPoints
WriteDenchar T
SaveRho T
SaveElectrostaticPotential T
SaveTotalPotential T
MeshCutoff 240.0 Ry

Then run denchar for wavefunctions and grid2cube for
charge density and potentials. In denchar input file,
use keywords LatticeConstant and LatticeVectors same as
in siesta input file. Keywords Denchar.{Min|Max}{X|Y|Z}
will be ignored. In grid2cube input file, 3rd and 4th
lines (shift of the origin of coordinates and nskip)
will be ignored.

There is also irrbz.py that extracts irreducible wedge
from siesta output files prefix.KP and prefix.EIG.
This is needed because siesta reduces k-points by
time-reversal symmetry only.


## MeanField/SIESTA/siesta2bgw.inp

 &input_siesta2bgw
systemlabel      = 'prefix'  ! SystemLabel used in SIESTA calculation
wfng_output_file = 'wfng.lo' ! file to write generated wavefunctions to
rhog_output_file = 'rhog.lo' ! file to write rho(G) (blank = not written)
vxcg_output_file = 'vxcg.lo' ! file to write Vxc(G) (blank = not written)
ecutwfn          = 0.0       ! kinetic energy cutoff (Ry) for wavefunctions
ecutrho          = 0.0       ! kinetic energy cutoff (Ry) for rho and V
wfng_nk1         = 0         ! number of k-points along b1
wfng_nk2         = 0         ! number of k-points along b2
wfng_nk3         = 0         ! number of k-points along b3
wfng_dk1         = 0.0       ! k-grid offset along b1 in units of b1/nk1
wfng_dk2         = 0.0       ! k-grid offset along b2 in units of b2/nk2
wfng_dk3         = 0.0       ! k-grid offset along b3 in units of b3/nk3
wfng_ref_flag    = .false.   ! shift eigenvalues to match reference state
wfng_ref_kpoint  = 0         ! reference state k-point index
wfng_ref_spin    = 0         ! reference state spin index
wfng_ref_band    = 0         ! reference state band index
wfng_ref_energy  = 0.0       ! reference state eigenvalue (in eV)
wfng_band_flag   = .false.   ! choose a range of bands (0 = all)
wfng_band_min    = 0         ! minimum band number
wfng_band_max    = 0         ! maximum band number
wfng_energy_flag = .false.   ! choose an energy window
wfng_energy_min  = 0.0       ! minimum energy (in eV)
wfng_energy_max  = 0.0       ! maximum energy (in eV)
wfng_gamma_real  = .false.   ! only real wavefunctions at the Gamma point
/



## Octopus

Octopus is a real-space DFT and TDDFT code available under the GPL from http://www.tddft.org/programs/octopus.
Support for BerkeleyGW output is implemented in Octopus since version 4.1.0.


## EPM


================================================================================

"The empirical pseudopotential method never lost a battle to experiment."
-- Marvin Cohen, 2008

================================================================================

EPM stands for Empirical Pseudopotential Method. It is the plane-wave
part of TBPW-1.1 modified to generate input files for BerkeleyGW.
Numerous other corrections and improvements have also been made
by Georgy Samsonidze and David Strubbe.

The input variables are described in epm.inp. Most variables are common to both
epm.x and epm2bgw.x, but a few are just for one or the other.

The real wavefunctions for systems with inversion symmetry
are obtained by applying the Gram-Schmidt process adapted from
paratecSGL-1.1.3/src/para/gwreal.f90

To plot silicon band structure calculated with the EPM executable:
% epm.x < silicon-epm.in
% gnuplot bands.plt
Uses variables NumberOfLines, NumberOfDivisions, KPointsAndLabels.

To use the explicit form factors and to compute the band gap and
the effective masses (mass only correct for Si-like band structures):
% epm.x < silicon-epm-ff.in
Uses variables gap_flag, gap_file, mass_flag, mass_file.

To generate input files for BerkeleyGW executable, use epm2bgw.x.
The scripts epm2bgw_cplx.sh and epm2bgw_cplx_spin.sh are just for use
with the testsuite. They force complex, or complex and spin-polarized.

You can find the actual input files for GW/BSE calculations on top of
EPM in directory examples/EPM, as well as testsuite directories
Si-EPM, GaAs-EPM, and Si-Wire-EPM.

The k-points for the EPM input files can be generated using utility

Virtual crystal approximation (VCA) is implemented within EPM in
the form of two pre-processing scripts, ff2vq.py and vca.py.

ff2vq.py reads EPM form factors from file form_factors.dat, fits them
to the chosen functional form of the V(q) potential, writes potential
coefficients to file v_of_q.dat, and writes new form factors computed
from V(q) to file vq2ff.dat. This procedure is described by equations
(8) and (9) and the accompanying text in Phys. Rev. B 84, 195201 (2011).

vca.py reads V(q) potential coefficients from file v_of_q.dat,
employs the virtual crystal approximation to compute hybrid form
factors, and writes them to file vca_ff.dat. The potential mixing
is controlled by identifiers host_material and doping_level hard
coded below. This procedure is described by equations (10) -- (12)
and the accompanying text in Phys. Rev. B 84, 195201 (2011).

The original form factors from file form_factors.dat or the hybrid
ones from file vca_ff.dat can be fed to epm.x and epm2bgw.x using
keywords LatticeConstant and FormFactors in the input file for epm.x
or epm2bgw.x. See example of using these keywords in silicon-epm-ff.in.

The README file of TBPW-1.1 follows below.

================================================================================

TBPW-1.1

========================================

Author/Affiliation

--------------------

* Dyutiman Das, UIUC
* William Mattson, UIUC
* Nichols A. Romero, UIUC
* Richard M. Martin, UIUC

========================================

Author email

--------------------

nromero@uiuc.edu

========================================

Description of Software

--------------------

TBPW is an electronic structure code primarily intended for pedagogical purposes. It is written from the ground-up in a modular style using Fortran 90. This code is composed of two distinct parts: a tightbinding (TB) and plane wave (PW). Additionally, there is a plane wave density (PWD) code which outputs the electron density on a grid.

The main characteristics of these codes are:

* Readily provides band structure plots
* TB implemented using a rotation matrix formalism allows the use of orbitals with arbitrary angular momentum l
* PW implemented using the option of diagonalisation via direct-inversion

Send email to tbpw-subscribe@mcc.uiuc.edu to subscribe to the mailing list, tbpw@mcc.uiuc.edu

This material is based upon work supported by the NSF under Award No. 99-76550 and the DOE under Award No. DEFG-96-ER45439

========================================

Submitted

--------------------

2003-01-31

========================================

Disclaimer

--------------------

Developed by Electronic Structure Group, University of Illinois, Department of Physics, http://www.physics.uiuc.edu/research/ElectronicStructure/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution.
* Neither the names of the Electronic Structure Group, the University of Illinois, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission.

THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.

========================================

--------------------

================================================================================



## MeanField/EPM/epm.inp

# BEWARE: you cannot comment out tags with # in EPM!
# any occurrence of a tag will be found and read.

# These parameters are only for epm2bgw
real_or_complex 1        # 1 = real, 2 = complex. default is complex.
wfng_flag T              # Write wavefunction file (default F)
wfng_file WFN            # filename (default WFN)
KPointNumbers 5 5 5      # number of points in k-grid in each direction b1,b2,b3
KPointOffsets 0.5 0.5 0.5 # shift in k-grid in each direction b1,b2,b3
rhog_flag T              # Write density file (default F)
rhog_file RHO            # filename (default RHO)
vxcg_flag T              # Write xc potential file (default F)
vxcg_file VXC            # filename (default VXC)
vxc_flag T               # Write VXC matrix element file (default F)
vxc_file vxc.dat         # filename (default vxc.dat)
vxc_diag_nmin 1          # minimum band to write diagonal matrix elements (default 0)
vxc_diag_nmax 8          # maximum band to write diagonal matrix elements (default 0)
vxc_offdiag_nmin 1       # minimum band to write off-diagonal matrix elements (default 0)
vxc_offdiag_nmax 8       # maximum band to write off-diagonal matrix elements (default 0)
disable_symmetries F     # set to true to write no symmetries (default F)
# EPM does not really do a spin-polarized calculation, but can write two copies of everything
nspin 1                  # set to 2 to write spin up and spin down (default 1)
FFTGrid 16 16 16         # FFT grid for computing density (default: determined from EnergyCutoff)

# These parameters are common to epm and epm2bgw
# Set form factor parameters (see examples in form_factors.dat),
# or default is to use V(q) from atomPotentialMod (only for H,Si,Ga,As)
FormFactors 5.43  -0.224  0.055  0.072  0.000  0.000  0.000

# 0 is for LAPACK direct diagonalization (default), 1 for conjugate gradients
DiagonalizationSwitch 0
AbsoluteTolerance -1.0d0  # tolerance for LAPACK diagonalization (default -1 means machine precision)
CGIterationPeriod 5       # parameter for conjugate gradients (default 3)
CGTolerance 1.0d-10       # parameter for conjugate gradients (1d-5)

InputEnergiesInEV          # Rydberg is default
EnergyCutoff 11.0          # plane-wave cutoff for the potential (and wavefunctions)

NumberOfDimensions 3              # dimensionality of the system (default 3)
#LatticeConstantFormat Angstrom   # default is Bohr
LatticeConstant 10.2612           # in units given above
LatticeVectors                    # in lattice constant units
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0

NumberOfAtoms 2
NumberOfSpecies 1
ChemicalSpeciesLabel              # index, atomic number, name
1 14 Si
AtomicCoordinatesFormat ScaledByLatticeVectors
# ScaledByLatticeVectors (default) is in crystal coordinates
# ScaledCartesian is in units of LatticeConstant
AtomicCoordinatesAndAtomicSpecies  # x, y, z, species index
-0.125 -0.125 -0.125 1
0.125  0.125  0.125 1

NumberOfBands 8
NumberOfOccupiedBands 4      # note: you cannot really do metals, occupations are fixed.

KPointsScale ReciprocalLatticeVectors # default; other choice is TwoPi/a
KPointsList 19          # number of k-points supplied
0.100000000  0.100000000  0.100000000  2.0  # kx, ky, kz, weight (will be renormalized)
0.100000000  0.100000000  0.300000000  6.0
0.100000000  0.100000000  0.500000000  6.0
0.100000000  0.100000000  0.700000000  6.0
0.100000000  0.100000000  0.900000000  6.0
0.100000000  0.300000000  0.300000000  6.0
0.100000000  0.300000000  0.500000000 12.0
0.100000000  0.300000000  0.700000000 12.0
0.100000000  0.300000000  0.900000000 12.0
0.100000000  0.500000000  0.500000000  6.0
0.100000000  0.500000000  0.700000000 12.0
0.100000000  0.500000000  0.900000000  6.0
0.100000000  0.700000000  0.700000000  6.0
0.300000000  0.300000000  0.300000000  2.0
0.300000000  0.300000000  0.500000000  6.0
0.300000000  0.300000000  0.700000000  6.0
0.300000000  0.500000000  0.500000000  6.0
0.300000000  0.500000000  0.700000000  6.0
0.500000000  0.500000000  0.500000000  1.0

# for plotting band structures; used if KPointsList not present
NumberOfLines 4
NumberOfDivisions 20
KPointsScale ReciprocalLatticeVectors # same as above
KPointsAndLabels
0.500 0.500 0.500 L
0.000 0.000 0.000 G
0.500 0.000 0.500 X
0.625 0.250 0.625 U
0.000 0.000 0.000 G

# These parameters are only for epm. Find band gap and effective mass.
gap_flag F              # default F
gap_file bandgap.dat    # filename (default gap.dat)
# Note: effective mass only works for silicon-like band structures.
mass_flag F             # default F
mass_file effmass.dat   # filename (default mass_file)


## ICM


This program reads the wavefunction file in Gaussian Cube or
XCrySDen XSF format and computes the Coulomb integral within
an image charge model.

It is based on Visual/surface.cpp code, so the input parameter
file formats for the two codes are quite similar. You can find
more details in Visual/surface.inp and Visual/README.

Input is read from file icm.inp:

inputfilename C6H6.b_15.cube
inputfileformat cube
threshold 0.99
threshold_power 1
coulomb_power 1
mirrorplaneorigin
0.0 0.0 -2.0
mirrorplanenormal
0.0 0.0 1.0
mirrorplaneunit angstrom
uc F
uco
0.0 0.0 0.0
ucv
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
ucu latvec
sc T
sco
-0.5 -0.5 -0.5
scv
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
scu latvec

In the above example, the HOMO wavefunction of benzene is read from
Gaussian Cube file. The wavefunction is placed in the center of the
supercell (see the meaning of uc, uco, ucv, ucu, sc, sco, scv, scu
parameters in Visual/surface.cpp). The parts of the wavefunction
outside an isosurface that contains 99% of the charge density are
dropped (parameters threshold and threshold_power have the same
meaning as isovalue and power in Visual/surface.cpp). Parameter
coulomb_power tells the code whether the wavefunction in the Coulomb
integral needs to be squared. Set both powers to 1 if the wavefunction
file contains the squared amplitude as produced by ESPRESSO, and to 2
for the linear amplitude as in PARATEC or SIESTA. The mirror plane
is defined by parameters mirrorplaneorigin and mirrorplanenormal,
in the above example it is parallel to the xy plane crossing the
z axis at -2 Angstrom. Problems may occur with non-orthogonal unit cells;
use of cubic cells is recommended.


## Utilities

-----------------------------------------------------------------
----------  MeanField Utilities  --------------------------------
-----------------------------------------------------------------

degeneracy_check.x:

Determine which numbers of bands do not break a degenerate subspace, to avoid warnings or
errors in Epsilon, Sigma, and BSE codes. Supply any number of binary WFN files as command-
line arguments, and a list of numbers that are acceptable for all k-points in all files
will be written to standard output.

mf_convert_wrapper.sh:

Converts WFN/RHO/VXC files between binary and ASCII. This can be useful for moving files
correctly between big- and little-endian machines, or for examining the contents of a
file (though wfn_rho_vxc_info.x is more user-friendly). Using this wrapper script, the
flavor (real/complex), type of file, and binary/ASCII is determined automatically.

wfn_rho_vxc_info.x:

Prints the contents of the header of a (binary) WFN, RHO, or VXC file in a clearly labeled
format, for human inspection.

wfnmerge.x:

Merges many WFN files into one. It assumes that all input files have the
same number and same ordering of G-vectors for the charge density.
The number and name of input files is read from "wfnmerge.inp", as well
is the kgrid and the kshift.

FAQ:
Q: Why would someone want to use this?
A: For example, maybe to do a converged calculation one needs to include a
large number of unoccupied states. There may not be the resources (either
CPUs or wallclock) to do this all in one shot, so it may be beneficial to
split up a calculation of kpoints (e.g., 4x4x4 MP grid) into smaller
pieces and then add up the final wavefunctions.
Q: What is the deal with kpoint weights?
A: Quantum Espresso renormalizes the kpoint weights that you use in a
calculation. If you are splitting up a MP grid into different groups of
kpoints, and each group is normalized, the relative weights between
kpoints in different groups is no longer correct. BerkeleyGW does not
make use of the kpoint weights (except for in determining whether the
Fermi level is reasonable for metallic calculations). So for most uses
the fact that these weights are incorrect does not matter. If it matters
to you, you can simply modify wfnmerge to read in the kpoint weights of

convert_old_to_new.x:

Convert wavefunction, density, and exchange-correlation potential files from the old
CWFE(q)/CD95/VXC formats (used in the pre-1.0 version of the code prior to June 2011)
to the current WFN/RHO/VXC formats. Some additional information is required which was not
available in the old files, so an input file convert_old_to_new.inp is required. See the
example in this directory. Input and output files are both binary.

scissors2eqpx:

Write an eqp.dat file based on a WFN file and scissors parameters.
For testing equivalence of eqp_corrections and scissors.

fix_occ.x:

Fix the occupations of a WFN file. This is useful if you have split a
large nscf calculations into smaller blocks, and you want the occupations
of the merged WFN to be consistent. It can also fix inconsistencies in the
occupations and in the Fermi energy for metals.

wfn_dotproduct.x

Form the overlap between the bands in two wavefunction files.
If they are copies of the same file, you can check orthonormality.
Only bands at corresponding k-points are considered, since
the overlap is zero by Blochs theorem if the k-points differ.
Warning: a known issue is possible errors from gmap when relating
k-points by symmetry operations.



## MeanField/Utilities/convert_old_to_new.inp

44.0 11.0
cubic
bohr
0.0000 5.1306 5.1306
5.1306 0.0000 5.1306
5.1306 5.1306 0.0000
crystal
2
-0.125 -0.125 -0.125 14
0.125  0.125  0.125 14
2 2 2

# example input file for convert_old_to_new.x for Si
# coordinates are crystal, in units of the lattice vectors
# Note: you need high precision in the lattice vectors
# so that the volume calculated from them matches the volume
# in the input file
# The kgrid in the last line is only read if the kgrid in
# the wfn file contains a zero, since pre-r307 paratec writes
# 0 0 0 for shifted grids.

# charge-density and wave-function cutoffs (in Ry)
# cubic or hexagonal symmetry group
# units of the lattice vectors (bohr, angstrom)
# a1x a1y a1z
# a2x a2y a2z
# a3x a3y a3z
# units of the atomic positions (bohr, angstrom, crystal)
# number of atoms
# x1, y1, z1, atomic number 1
# x2, y2, z2, atomic number 2
# etc.
# kgrid_x kgrid_y kgrid_z


## MeanField/Utilities/wfnmerge.inp

WFN.OUT     ! name of output WFN file
4 4 4       ! final k-grid
0.0 0.0 0.0 ! final k-shift
2           ! total number of input WFN files
8           ! total number of k-points in all input WFN files
wfn_0/WFN   ! name of 1st input WFN file
wfn_1/WFN   ! name of 2nd input WFN file
1.0         ! relative weight of 1st input WFN file
1.0         ! relative weight of 2nd input WFN file


## MeanField/Utilities/fix_occ.inp

WFN_in  ! input  WFN
WFN_out ! output WFN
0       ! original number of electrons in WFN_in (0 to autodetect)
0       ! extra charge to put in


## SAPO


The SAPO (Simple Approximate Physical Orbitals) code reads DFT
wavefunctions from WFN file, generates additional wavefunctions on top
of them, and writes both to another WFN file. It can generate plane waves,
decompose them into irreducible representations of the space group of the
Bravais lattice or the crystal, and orthonormalize them with respect to
DFT wavefunctions. It can insert SIESTA wavefunctions read from auxiliary
WFN file in between plane waves and orthonormalize them altogether.
It can apply a random variation to the plane waves and SIESTA wavefunctions
or generate completely random wavefunctions and orthonormalize them.
It can correct eigenvalues during orthonormalization or perform subspace
diagonalization. It can drop the plane waves and SIESTA wavefunctions which
have a large overlap with DFT wavefunctions. It can keep wavefunctions with
the eigenvalues in a given energy range. It can extract eigenvalues and
plane wave coefficients from WFN file for plotting purposes.

The SAPO method is described in Phys. Rev. Lett. 107, 186404 (2011)

2012-12-24 (gsm): added iterative Davidson diagonalization, see
examples/DFT/Si2_sapo for details

Note: When using iterative Davidson diagonalization, it is recommended
to generate VXC rather than vxc.dat in pw2bgw run, then compute matrix
elements of VXC between SAPO wavefunctions. This is more consistent
than using vxc.dat because vxc.dat is computed between ESPRESSO
wavefunctions, and those might be slightly different from SAPO
wavefunctions.

Note: wfng_input_file should contain all occupied orbitals (and may or
may not contain some unoccupied orbitals), otherwise occupations written
to wfng_output_file will be wrong.

Note: Symmetrization of planewaves (sapo_symmetry .gt. 0) has no effect
on a SAPO calculation since it is just a linear combination in a degenerate
subspace. It is currently disabled because it requires symmetry subroutines
from Quantum ESPRESSO. To enable it open MeanField/SAPO/pw.f90, comment out
die, and uncomment s_axis_to_cart, find_group, set_irr_rap, divide_class.

Input is read from file sapo.inp:

&input_sapo
wfng_input_file = 'wfng.in'
wfng_aux_file = ''
vlr_input_file = ''
vnlg_input_file = ''
wfng_output_file = 'wfng.out'
sapo_band_number = 0
sapo_planewave_min = 1
sapo_planewave_max = 580
sapo_energy_shift = 0.0
sapo_energy_match = .true.
sapo_symmetry = 2
sapo_print_ir = .true.
aux_flag = .false.
aux_band_min = 0
aux_band_max = 0
aux_energy_shift = 0.0
sapo_random = 1
sapo_random_ampl = 1.0d-3
sapo_overlap_flag = .false.
sapo_overlap_max = 0.0
sapo_orthonormal = .true.
sapo_ortho_block = 0
sapo_ortho_order = 0
sapo_ortho_energy = .false.
sapo_energy_sort = .false.
sapo_hamiltonian = .false.
sapo_energy_range = .false.
sapo_energy_min = 0.0
sapo_energy_max = 0.0
sapo_check_norm = .false.
sapo_plot_kpoint = 0
sapo_plot_spin = 0
sapo_plot_bandmin = 0
sapo_plot_bandmax = 0
sapo_plot_pwmin = 0
sapo_plot_pwmax = 0
sapo_eigenvalue = .false.
sapo_projection = 0
sapo_amplitude = .false.
sapo_ampl_num = 0
sapo_ampl_del = 0.0
sapo_ampl_brd = 0.0
/

Here, the wavefunctions are read from wfng.in file and written to wfng.out
file. The parameter sapo_band_number specifies the number of wavefunctions
to be read from the input file (if set to 0 all the wavefunctions will be
read). The PW wavefunctions will be constructed from plane waves ranging
from 1 (sapo_planewave_min) to 580 (sapo_planewave_max). The kinetic energies
of the plane waves will be shifted to match the eigenvalues of the input
wavefunctions (sapo_energy_match). The plane waves will be decomposed into
irreducible representations of the space group of the Bravais lattice
(sapo_symmetry = 2), and the decomposition will be printed to the standard
output (sapo_print_ir). The auxiliary wavefunctions will not be inserted in
between the PW wavefunctions (aux_flag). A random variation (sapo_random = 1)
with a small amplitude (sapo_random_ampl = 1.0d-3) will be added to the PW
wavefunctions. The PW wavefunctions will be orthonormalized with respect
to the valence and conduction bands (sapo_orthonormal) in the ascending
order with respect to energy (sapo_ortho_order = 0). The orthonormality
check will not be performed (sapo_check_norm). The energy eigenvalues,
the projections of wavefunctions onto plane waves, and the squared
absolute values of amplitudes of the wavefunctions with respect to
kinetic energies of plane waves will not be plotted (sapo_eigenvalue,
sapo_projection, and sapo_amplitude).

The auxiliary wavefunctions can be used in two different ways:

(1) Use hybrid valence wavefunctions as wfng_input_file and LDA conduction
wavefunctions as wfng_aux_file, set sapo_planewave_min and sapo_planewave_max
to 0, sapo_orthonormal to .true. and sapo_ortho_block to 1. This way you will
get a good starting point for nscf hybrid calculations in PARATEC or ESPRESSO.

(2) Use Siesta wrapper in MeanField/SIESTA directory to construct the resonant
states from SIESTA wavefunctions (look into MeanField/SIESTA/README for details
on how to use siesta2bgw), feed them to the SAPO code through wfng_aux_file
parameter, and generate continuum states from plane waves by setting
sapo_planewave_max to a large number. Also set sapo_orthonormal,
sapo_ortho_block and sapo_ortho_order to orthonormalize the resonant and
continuum states in the desired order with respect to the bound states
from PARATEC or ESPRESSO. You may want to set sapo_ortho_energy to .true.
for correcting the eigenvalues during the orthonormalization, or to set
sapo_hamiltonian to .true. for correcting both the wavefunctions and
the eigenvalues by diagonalizing the Hamiltonian. The latter requires
the local potential file in Gaussian Cube format (vlr_input_file),
and optionally the non-local pseudopotential file (vnlg_input_file).
Finally, set sapo_energy_sort to .true. for sorting the resonant
and continuum states by their eigenvalues before writing them
to the output file. You may also set sapo_energy_range to .true.
for keeping the eigenvalues in the energy range of sapo_energy_min
to sapo_energy_max.

PS: If you don't know or don't want to manually set
sapo_planewave_min and aux_band_min, set both of them to 1,
sapo_overlap_flag to .true., and sapo_overlap_max to 0.3.
This will automatically throw away plane-waves and auxiliary
states that have large overlaps (scalar products > 0.3)
with DFT states and among themselves. The scalar products
of PW and AUX states with DFT states will be written to files
overlap_dft_k#_s#.dat, and the scalar products of PW states
with AUX states will be written to files overlap_aux_k#_s#.dat,
so you can inspect what states were thrown away after the run.
This useful feature is informally known as boverlap, in honor
of Brad Malone who first proposed this idea. This confirms
once again that evolution is a byproduct of laziness.



## MeanField/SAPO/sapo.inp

&input_sapo
wfng_input_file = 'wfng.pw' ! file to read DFT wavefunctions from
wfng_aux_file = 'wfng.lo'   ! file to read auxiliary wavefunctions from
vscg_input_file = 'vscg'    ! file to read self-consistent potential
! in G-space for constructing Hamiltonian
! (generated by pw2bgw.x from Quantum ESPRESSO)
vkbg_input_file = 'vkbg'    ! file to read Kleinman-Bylander projectors
! in G-space for constructing Hamiltonian
! (generated by pw2bgw.x from Quantum ESPRESSO)
wfng_output_file = 'wfng'   ! file to write generated wavefunctions to
sapo_band_number = -1       ! number of DFT wavefunctions to use
! (set to -1 to use all wavefunctions found
! in wfng_input_file)
sapo_planewave_min = 0      ! indices of the lowest and highest plane waves
sapo_planewave_max = 0      ! to construct wavefunctions from (0 = none)
sapo_energy_shift = 0.0     ! energy shift for PW kinetic energies (eV)
sapo_energy_match = .false. ! match PW kinetic energies & DFT eigenvalues
sapo_symmetry = 0           ! 0 = none, 1 = crystal, 2 = lattice symmetry
sapo_print_ir = .false.     ! print irreducible representations of PW
aux_flag = .false.          ! insert auxiliary wavefunctions in between PW
aux_band_min = 0            ! minimum and maximum band indices of auxiliary
aux_band_max = 0            ! wavefunctions (0 = all)
aux_energy_shift = 0.0      ! energy shift for auxiliary eigenvalues (eV)
sapo_random = 0             ! 0 = none, 1 = small variation, 2 = random
sapo_random_ampl = 0.0      ! amplitude of the random variation
sapo_random_norm = .false.  ! normalize randomized wavefunctions
sapo_overlap_flag = .false. ! drop PW & AUX states that have a large
! overlap with DFT states
sapo_overlap_max = 0.0      ! maximum scalar product of PW & AUX with DFT
sapo_orthonormal = .false.  ! orthonormalize PW & AUX wavefunctions wrt DFT
sapo_ortho_block = 0        ! 0 = PW/AUX, 1 = AUX/PW, 2 = ordered in energy
sapo_ortho_order = 0        ! 0 = ascending, 1 = descending order in energy
sapo_ortho_energy = .false. ! correct PW & AUX eigenvalues by perturbative
! approach during orthonormalization
sapo_energy_sort = .false.  ! sort PW & AUX eigenvalues in ascending order
sapo_hamiltonian = .false.  ! correct PW & AUX wavefunctions & eigenvalues
! by diagonalizing subspace Hamiltonian or
! by iteratively diagonalizing Hamiltonian
sapo_ham_nrestart = 0       ! maximum number of iterative diagonalization
! restarts with random initial wavefunctions
! for k-points/spins that didnt converge
sapo_ham_ndiag = 0          ! maximum number of subspace diagonalization
! steps during iterative diagonalization
sapo_ham_ndim = 0           ! maximum number of basis functions in units
! of the total number of wavefunctions,
! same as diago_david_ndim in pw.x
sapo_ham_tol = 0.0          ! tolerance on the maximum norm of residual
! vectors for iterative diagonalization (Ry)
sapo_ham_resinc = .false.   ! stop expanding the basis set and update
! the wavefunctions when the maximum norm
! of residual vectors starts increasing
sapo_do_all_bands = .false. ! orthonormalize and diagonalize DFT & PW & AUX
! wavefunctions or PW & AUX wavefunctions
sapo_energy_range = .false. ! keep PW & AUX eigenvalues in the energy range
sapo_energy_min = 0.0       ! minimum energy for PW & AUX eigenvalues (Ry)
sapo_energy_max = 0.0       ! maximum energy for PW & AUX eigenvalues (Ry)
sapo_check_norm = .false.   ! check orthonormality of wavefunctions
sapo_plot_kpoint = 0        ! k-point index (0 = all) for output plots
sapo_plot_spin = 0          ! spin index (0 = all) for output plots
sapo_plot_bandmin = 0       ! range of band indices (0 = all) for output
sapo_plot_bandmax = 0       ! eigenvalue, projection and amplitude plots
sapo_plot_pwmin = 0         ! range of plane wave indices (0 = all) for
sapo_plot_pwmax = 0         ! output projection plots
sapo_eigenvalue = .false.   ! plot energy eigenvalues wrt band index (eV)
sapo_projection = 0         ! plot projections of wavefunctions onto PW
! 0 = none, 1 = wrt band, 2 = wrt PW, 4 = both
sapo_amplitude = .false.    ! plot squared absolute values of amplitudes of
! wavefunctions wrt kinetic energies of PW (Ry)
sapo_ampl_num = 0           ! number of points on the kinetic energy scale
sapo_ampl_del = 0.0         ! separation between the adjacent points (Ry)
sapo_ampl_brd = 0.0         ! broadening for wavefunction amplitudes (Ry)
/


## Epsilon

-----------------------------------------------------------------
----------  GW code, Epsilon  -----------------------------------
-----------------------------------------------------------------

Version 1.1   (June, 2014)

Version 1.0	(September, 2011)
Version 0.5	J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008)
Version 0.2	S. Ismail-Beigi (2002)
Version 0.1	G. M. Rignanese, E. Chang, X. Blase  (1998)
Version 0.0	M. Hybertsen (1985)

-----------------------------------------------------------------

Description:

Epsilon is the name of the code that generates the polarizability matrix and
the inverse dielectric matrix for a bulk or nanoscale system. The main
result of the Epsilon code is the generation of epsmat which can be used
in a Sigma or BSE calculation.

-----------------------------------------------------------------

Required Input:

epsilon.inp	Input parameters. See example in this directory.
WFN		This is linked to the unshifted grid.
WFNq		This is linked to the shifted grid.
When a shift is not required, this can be the same file as WFN
(i.e. for semiconductor or graphene screening with spherical or
box truncation).

Auxiliary Files: (output files from previous runs, used as input to speed up calculation)

chimat		Polarizability matrix. No need to recalculate matrix elements.
chi0mat		Polarizability matrix at q=0. No need to recalculate matrix elements.

The files below are used if eqp_corrections is set in epsilon.inp.
The corrected eigenvalues are used for constructing the polarizability matrix.
eqp.dat         A list of quasiparticle energy corrections for the bands in WFN.
eqp_q.dat       A list of quasiparticle energy corrections for the bands in WFNq.

-----------------------------------------------------------------

epsilon.inp	Please see example epsilon.inp in this directory
for more complete options.

-----------------------------------------------------------------

Output Files:

espmat			Inverse dielectric matrix (q<>0).
eps0mat			Inverse dielectric matrix (q->0).

or

espmat.h5		Equivalent of above when using HDF5
eps0mat.h5		For specification, see epsmat.h5.spec

epsilon.log		The log file containing values of chimat and epsmat.
chi_converge.dat	Convergence chi with respect to empty orbitals.
Columns: number of conduction bands,
Re chi(G=0,G'=0,q),     extrapolated Re chi(G=0,G'=0,q),
Re chi(G=Max,G'=Max,q), extrapolated Re chi(G=Max,G'=Max,q)

-----------------------------------------------------------------

Tricks and hints:

1. Comments on convergence of epsilon_cutoff

There are many ways to check convergence of this parameter:

-Ideally, the inverse epsilon matrix is almost diagonal for large
G vectors. So, for small ( G , G' ) it is usually large but, for
G or G' close to G_max, it is smaller by a factor of 100, more or
less. Check if the ratio between the greatest and lowest matrix
elements is large.

-Alternatively, one can check if epsinv( G_max , G'_max ) is close
to 1 for G = G'. It should be about 0.999 or so. Note that 0.9 isn't
"close to 1" in this case! Also check if epsinv( G_max , G'_max ) is
indeed small for G != G'.

2. Comments on the null point

The null point (Gamma point) is treated in a special manner. In input,
declare it as slightly shifted from the true Gamma point:

0.0000    0.0050    0.0050   1.0   1

This is the only k-point with itestq=1 instead of 0!

The magnitude of this vector must be small: of order 0.01 or smaller
for less than 100 points in full Brillouin zone. If the density
of points in BZ increases, that magnitude should decrease accordingly.

3. Macroscopic dielectric constant

In GW, the screened interaction gives the formula:

eps(G,G';q) = delta_GG' - [4pi e^2/(q+G)^2 ] chi(G,G';q)

where chi(G,G';q) is the polarizability (P in the literature).

if G=0  and q=0

then we let

eps(0,G';q) = delta_0G' - lim(q->0) [4pi/(q)^2] chi(0,G';q)

always check chi(0,0;q->0) and eps^(-1)(0,0;q->0)
in epsilon.log

1/eps^(-1)(0,0;q->) should be the macroscopic epsilon,
local-field effects
1/(1-4*pi*chi(0,0;q->0)*V_c(0) should also be (roughly) the macroscopic epsilon,
without local-field effects

4. Merging epsmat files

The Epsilon code is complicated and involves lots of computation. Frequently,
it is useful to calculate the epsilon matrix for a small number
of q-points, and later put all those pieces of matrix into a big
epsmat file. Use epsmat_merge to do this. See below.

Notes:
-epsilon cutoff *must* be the same for all files to be merged
-The ordering of q-points in the input file must correspond to the ordering of
epsmat files: the first file has the first set of points, the second file
has the second and so on.

5. Utilities:

----------------------------------------------------------------------
---------  epsmat, eps0mat binary/ASCII conversion  ------------------
----------------------------------------------------------------------

TOOLS: epsbinasc, epsascbin

USAGE: simply type name of executable.

The input file is named epsconv.inp.

----------------------------------------------------------------------
--------  WFN/RHO/VXC binary/ASCII conversion ------------------------
----------------------------------------------------------------------

TOOL: mf_convert_wrapper.sh

USAGE: ./mf_convert_wrapper.sh infile outfile

Real/complex, bin/asc, file type, is automatically detected.

----------------------------------------------------------------------
---------  epsmat merging  -------------------------------------------
----------------------------------------------------------------------

TOOL: epsmat_merge

USAGE: epsmat_merge.[real/cplx].x

Merges the content of multiple binary epsmat files into an output file
called 'epsmat', concatenating data. See input file epsmat_merge.inp,
for specification of cutoff, q-points, and input epsmat filenames.


## Epsilon/epsilon.inp

# epsilon.inp

# G-vectors will be used with kinetic energies up to this cutoff (Ry)
epsilon_cutoff           8.0

# number of bands to sum over
number_bands             146

# a list of which bands are occupied (1) and which are unoccupied (0)
band_occupation          18*1 128*0

# If you have partially occupied bands (Metal) set
# number_partial_occup to the number of these bands.
# And set occupation of these bands to zero in the
# band_occupation line above.
# (this is former ncrit)
#number_partial_occup    0

# Specify the Fermi level (in eV), if you want implicit doping
# Note that value refers to energies AFTER scissor shift or eqp corrections.
#fermi_level             0.0

# The Fermi level is treated as an absolute value
# or relative to that found from the mean field (default)
#fermi_level_absolute
#fermi_level_relative

# RECOMMENDED fast FFTW truncation schemes
# The Coulomb Interaction is cutoff on the edges of
# the Wigner-Seitz Cell in the non-periodic directions
# Periodic directions are a1,a2 for slabs and a3 for wires

#cell_box_truncation
#cell_wire_truncation
#cell_slab_truncation

# Analytic, but non-Wigner-Seitz Cell Truncation

#spherical_truncation

# For Spherical Truncation, radius in Bohr

# Frequency dependence of the inverse dielectric matrix.
# Set to 0 to compute the static inverse dielectric matrix (default).
# Set to 2 to compute the full frequency dependent inverse dielectric matrix.
#frequency_dependence 0

# Full frequency dependence method for the polarizability.
# set to 0 for the Adler-Wiser formula (default).
# set to 1 for the Shishkin and Kresse, Phys. Rev. B 74, 035101, 2006.
# WARNING: the Shishkin and Kresse method is still under development. Always
#frequency_dependence_method 0

# Parameters for the full frequency dependent inverse dielectric matrix.
# All are in units of eV.
# Specify the initial frequency, the initial frequency increment,
#
# init_frequency should always be set to zero, delta_frequency to a small
# positive real number, broadening to a small positive real number close to delta_frequency
#
# The frequency cutoffs work in the following way: Up until the low_cutoff, the frequency grid will be
# uniform and spaced by delta_frequency.  After the frequency_low_cutoff, the frequency grid will
# begin to be more sparse with the grid spacing increasing by an amount delta_frequency_step
# after each grid point.  The frequency grid is truncated all together after the frequency_high_cutoff.
#
# Default settings:
# frequency_high_cutoff = 4*frequency_low_cutoff
# delta_frequency_step = 1.0 eV
#
# Suggestion:
# frequency_low_cutoff = energy of highest unoccupied state - energy of lowest occupied state
#
# For example,
#init_frequency 0.0
#delta_frequency 0.2
#delta_frequency_step 1.0
#frequency_low_cutoff 125.0
#frequency_high_cutoff 500.0

# When setting frequency_dependence 2 and frequency_dependence_method 1,
# use the following parameters for the spectral functions of the polarizability
# on a frequency grid.

# Notes:
# - Only "gcomm_elements" is supported with the Shishkin and Kresse full-
#   frequency-dependence implementation
# - For accuracy, set "sfrequency_high_cutoff" as the largest transition energy,
#   i.e., (energy of highest unoccupied state) - (energy of lowest occupied state)

# Default settings:
# init_sfrequency=0.0
# delta_sfrequency=delta_frequency
# delta_sfrequency_step=0.0 (It means that uniform frequency grid is used.)
# sfrequency_low_cutoff=1.0 eV
#  (sfrequency_low_cutoff can be any value in [0.0,sfrequency_high_cutoff])
# sfrequency_high_cutoff=frequency_low_cutoff

# For example,
#init_sfrequency 0.0
#delta_sfrequency 0.2
#delta_sfrequency_step 0.0
#sfrequency_low_cutoff 1.0
#sfrequency_high_cutoff 125.0

# Logging convergence of the head & tail of polarizability matrix with respect to conduction bands.
# Set to -1 for no convergence test
# Set to 0 for the 5 column format including the extrapolated values (default).
# Set to 1 for the 2 column format, real part only.
# Set to 2 for the 2 column format, real and imaginary parts.
#full_chi_conv_log -1

# qx qy qz 1/scale_factor is_q0
# scale_factor is for specifying values such as 1/3
# is_q0 = 1 for a small q-vector in semiconductors
# is_q0 = 2 for a small q-vector in metals
# is_q0 = 0 for non-zero q-vectors
# if present the small q-vector should be first in the list
# You can generate this list with kgrid.x: just set the shifts to zero and use
# same grid numbers as for WFN. Then replace the zero vector with q0.
number_qpoints  16
begin qpoints
0.000000    0.000000    0.005000   1.0   1
0.000000    0.000000    0.062500   1.0   0
0.000000    0.000000    0.125000   1.0   0
0.000000    0.000000    0.187500   1.0   0
0.000000    0.000000    0.250000   1.0   0
0.000000    0.000000    0.312500   1.0   0
0.000000    0.000000    0.375000   1.0   0
0.000000    0.000000    0.437500   1.0   0
0.000000    0.000000    0.500000   1.0   0
0.000000    0.000000    0.562500   1.0   0
0.000000    0.000000    0.625000   1.0   0
0.000000    0.000000    0.687500   1.0   0
0.000000    0.000000    0.750000   1.0   0
0.000000    0.000000    0.812500   1.0   0
0.000000    0.000000    0.875000   1.0   0
0.000000    0.000000    0.937500   1.0   0
end

# Scissors operator (linear fit of the quasiparticle
# energy corrections) for the bands in WFN and WFNq.
# e_cor = e_in + es + edel * (e_in - e0)
# Defaults below. evs, ev0, ecs, ec0 are in eV.
# If you have eqp.dat and eqp_q.dat files
# this information is ignored in favor of the eigenvalues
# in eqp.dat and eqp_q.dat.
#evs     0.0
#ev0     0.0
#evdel   0.0
#ecs     0.0
#ec0     0.0
#ecdel   0.0
# or
#cvfit   0.0 0.0 0.0 0.0 0.0 0.0

# Set this to use eigenvalues in eqp.dat and eqp_q.dat
# If not set, these files will be ignored.
#eqp_corrections

# Write the bare Coulomb potential V(q+G) to file
#write_vcoul

# Matrix Element Communication Method (Chi Sum Comm)
# Default is gcomm_matrix which is good if nk*nc*nv > nmtx*nfreq
# If nk*nc*nv < nfreq*nmtx (nk*nv < nfreq since nc~nmtx),
# use gcomm_elements
gcomm_matrix
#gcomm_elements

# Communication through MPI or DISK
# comm_mpi is usually much faster and preferable but if you have only
# a few CPUs you might not have enough memory to hold wavefunctions
# comm_disk results in temporary INT_* files being created and it
# may be faster for a small unit cell and a lot of k-points
# The default is comm_mpi
comm_mpi
#comm_disk

# Number of pools for distribution of valence bands
# The default is chosen to minimize memory in calculation
#number_valence_pools 1

# By default, the code computes the polarizability matrix, constructs
# the dielectric matrix, inverts it and writes the result to file epsmat.
# Use keyword skip_epsilon to compute the polarizability matrix and
# write it to file chimat. Use keyword skip_chi to read the polarizability
# matrix from file chimat, construct the dielectric matrix, invert it and
# write the result to file epsmat.
#skip_epsilon
#skip_chi

# Use traditional simple binary format for epsmat/eps0mat instead of HDF5 file format.
# Relevant only if code is compiled with HDF5 support.
#dont_use_hdf5

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY
# 'unfolded BZ' is from the kpoints in the WFN file
# 'full BZ' is generated from the kgrid parameters in the WFN file
# See comments in Common/checkbz.f90 for more details
# Replace unfolded BZ with full BZ
#fullbz_replace
# Write unfolded BZ and full BZ to files
#fullbz_write

# The requested number of bands cannot break degenerate subspace
# Use the following keyword to suppress this check
# Note that you must still provide one more band in
# wavefunction file in order to assess degeneracy
#degeneracy_check_override

# Instead of using the RHO FFT box to perform convolutions, we automatically
# determine (and use) the smallest box that is compatible with your epsilon
# cutoff. This also reduces the amount of memory needed for the FFTs.
# Although this optimization is safe, you can disable it by uncommenting the
# following line:
#no_min_fftgrid



## Epsilon/epsconv.inp

#----------------------------
# Example epsconv.inp for epsbinasc/epsascbin.

# number of q-points
# output filename
# number of input files (will be merged)
# input filenames

1
epsmat.out
1
epsmat.in


## Epsilon/epsomega.inp

eps0mat      ! epsmat file, full-frequency or static
RHO          ! RHO file for Plasmon-Pole
0.0 0.0 0.0  ! q-vector in crystal coordinates
1 0 0        ! G-vector in crystal coordinates
1 0 0        ! G-vector in crystal coordinates
201          ! nFreq, for static epsmat. For full-freq., overwritten from file
0.5          ! dDeltaFreq in eV, in case of static epsmat. See above.
2.0          ! dBrdning in eV, in case of static epsmat. See above.
epsPP.dat    ! Plasmon-Pole epsilon, Re and Im parts
epsR.dat     ! Retarded epsilon, Re and Im parts
epsA.dat     ! Advanced epsilon, Re and Im parts


## Epsilon/epsinvomega.inp

eps0mat(.h5) ! epsmat file, full-frequency or static
RHO          ! RHO file for Plasmon-Pole
0.0 0.0 0.0  ! q-vector in crystal coordinates
1 0 0        ! G-vector in crystal coordinates
1 0 0        ! G-vector in crystal coordinates
201          ! nFreq, for static epsmat. For full-freq., overwritten from file
0.5          ! dDeltaFreq in eV, in case of static epsmat. See Above.
2.0          ! dBrdning in eV, in case of static epsmat. See Above.
0.1          ! Exciton binding energy to use to calculate the effective eps^-1 head for BSE.
epsInvPP.dat ! Plasmon-Pole epsilon inverse, Re and Im parts
epsInvR.dat  ! Retarded epsilon inverse, Re and Im parts
epsInvA.dat  ! Advanced epsilon inverse, Re and Im parts


## Epsilon/epsmat_merge.inp

44 7 ! ecuts1, nqtot
0.0000  0.0000  0.5000  1.0 ! qx qy qz div
0.0000  0.2500  0.0000  1.0
0.0000  0.2500  0.5000  1.0
0.0000  0.5000  0.0000  1.0
0.0000  0.5000  0.5000  1.0
0.2500  0.5000  0.0000  1.0
0.2500  0.5000  0.5000  1.0
1 ! nfiles
epsmat ! filename(i), i=1,nfiles


## Epsilon/epsmat_old2hdf5.inp

epsmat       ! Name of input file
epsmat.h5  ! Name of output file
5            ! Number of qpoints in file


## Sigma

-----------------------------------------------------------------
----------  GW code, Sigma  -------------------------------------
-----------------------------------------------------------------

Version 1.1	(June, 2014)
Version 1.0	(September, 2011)

Version 0.5	J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008)
Version 0.2	S. Ismail-Beigi (2002)
Version 0.1	G. M. Rignanese, E. Chang, X. Blase  (1998)
Version 0.0	M. Hybertsen (1985)

-----------------------------------------------------------------

Description:

Sigma is the second half of the GW code.  It should be run after
calculating epsmat/esp0mat in Epsilon.  It gives the quasiparticle
self-energies and dispersion relation for quasielectron and
quasihole states.  The main result is written to sigma.log file.

-----------------------------------------------------------------

Required Input:

sigma.inp	Input parameters.  See example in this directory.
epsmat(.h5)	Inverse dielectric matrix (q<>0).  Created using Epsilon.
eps0mat(.h5)	Inverse dielectric matrix (q->0).  Created using Epsilon.
WFN_inner	Real or complex wavefunctions. k-grid should be the same as
the q-grid of epsmat, though there can be a shift.
This is usually the reduced points from an
unshifted grid, i.e. PARATEC is called with no kgrid_shift.
RHO		Charge density (for generalized plasmon-pole model).
Produced by PARATEC using gwscreening on same grid
as WFN_inner.
vxc.dat		Matrix elements of the exchange-correlation potential,
from a mean-field calculation or a previous Sigma run.
VXC file may be used instead via keyword dont_use_vxcdat.

WFN_outer		Outer wavefunctions between which the
self-energy operator and exchange-correlation
potential are sandwiched. If absent inner
wavefunctions will be used instead. Note that
VXC should be consistent with outer wfn while
RHO with inner wfn. If outer wfn is generated
using a hybrid functional VXC contains the
local part of exchange-correlation potential.
In this case set bare_exchange_fraction in
sigma.inp to compensate for the non-local part,
or use vxc.dat instead of VXC.

The file below will be read only if eqp_corrections is set in sigma.inp.
eqp.dat			A list of quasiparticle energy corrections
for the bands in WFN_inner.
The corrected eigenvalues are used for
constructing the self-energy operator.

The file below will be read only if eqp_outer_corrections is set in sigma.inp.
eqp_outer.dat		A list of quasiparticle energy corrections for
the bands in WFN_outer.
The corrected eigenvalues determine
the energies at which the self-energy
operator is calculated.

Auxiliary Files:

x.dat		Matrix elements of the bare exchange, generated by a previous
Sigma run to speed up subsequent calculations.
Read if use_xdat keyword is present, written otherwise.
VXC		Exchange-correlation potential (whose matrix elements
are subtracted from DFT eigenvalues). Produced by
mean-field code, on same grid as WFN_inner.
Used only if vxc.dat is not present or keyword dont_use_vxcdat is set.

-----------------------------------------------------------------

sigma.inp	Please see example sigma.inp in this directory
for more complete options.

-----------------------------------------------------------------

Output Files:

sigma.log	The log file containing quasiparticle energy values
for desired states. For a full-frequency calculation
only the value for Sigma calculated at energy closest
to the outer wavefunction eigenvalue is shown. The file
spectrum.dat contains the full Sigma(E) spectra.

sigma_hp.log	High-precision version of sigma.log

ch_converge.dat Convergence of Sigma_ch with respect to empty orbitals.

spectrum.dat	The real and imaginary parts of Sigma as a function of
energy. The energy grid is specified in sigma.inp. This
file is only output in full-frequency calculations.
Some general notes:

* IM(SIGMA) was calculated using the same broadening
as RE(SIGMA), while IM(SIGMA2) was calculated without

There are 4 Sigmas currently reported.

1. Sigma = SX + CH with broadening in the CH Integral.
2. Sigma = SX + CH with no Broadening. We do the energy
denominator integral analytically.
3. Sigma = X + COR with broadening in the COR integral.
4. Sigma = X + COR with no broadening. We do the energy
denominator integral analytically.

* Ew is not the same as the frequencies specified in
sigma.inp. Ew is the absolute off-shell quasiparticle
energy, and it is *not* measured wrt the Fermi energy.
The (physically meaningful) on-shell quasiparticle
energy EQP is the solution of Dyson's equation:
Ew = E_LDA - Vxc + Re[Sig(Ew)].

-----------------------------------------------------------------

A Note About the Wings of Epsilon (for Semiconductors Only):

The wings of Chi have terms of the following form:

< vk | e^(i(G+q)r) | ck+q >< ck+q | e^(-iqr) | vk > (1)

The matrix element on the right is < u_ck+q | u_vk > where u is the periodic part
of the Bloch function. From k.p perturbation theory, this matrix element is proportional
to q. The matrix element on the left with a non-zero G is typically roughly
a constant as a function of q for small q (q being a small addition to G).

Thus for a general G-vector, Chi_wing(G,q) \propto q. This directly leads
to the wings of the screened untruncated Coulomb interaction being proportional
to 1/q. Note that this function changes sign as q -> -q. Thus, when treating the
q=0 point, we set the value of the wing to zero (the average of its value in the
mini-Brillouin zone (mBZ).

For G-vectors on high-symmetry lines, some of the matrix elements on the left of (1)
will be zero for q=0, and therefore proportional to q. For such cases,
Chi_wing(G,q) \propto q^2, and the wings of the screened Coulomb interaction
are constant as a function of q. However, setting the q->0 wings to zero still
gives us, at worst, linear convergence to the final answer with increased k-point
sampling, because the q->0 point represents an increasingly smaller area in the
BZ. Thus, we still zero out the q->0 wings, as discussed in
A Baldereschi and E Tosatti, Phys. Rev. B 17, 4710 (1978).

In the future, it may be worthwhile to have the user calculate chi / epsilon at
two q-points (a third q-point at q=0 is known) in order to compute the linear
and quadratic coefficients of each chi_wing(G,q) so that all the correct analytic
limits can be taken. This requires a lot of messy code and more work for the user
for only marginally better convergence with respect to k-points (the wings tend
to make a small difference, and this procedure would matter for only a small set
of the G-vectors).

It is important, as always, for the user to converge their calculation
with respect to both the coarse k-point grid used in sigma and kernel as well
as with the fine k-point grid in absorption.

-JRD+MJ

-----------------------------------------------------------------

Tricks and hints:

1. Comments on convergence of scc (screened_coulomb_cutoff)
and bcc (bare_coulomb_cutoff)

The parameters scc and bcc are independent to each other and are
related to the number or terms taken into account in the
plane-wave expansion of Sigma_(SEX + COH) and V_xc, respectively.

Since Sigma_(SEX) is related to epsilon, scc should be equal to
or less than the epsilon_cutoff used to compute chi0 and epsilon.

If you are to use large values for scc and bcc (say 50 Ry or so),
a good suggestion is run the sigma code twice: first with large
bcc and small scc, just to get x.dat and vxc.dat; then with large
scc and any bcc, using the x.dat and vxc.dat files generated before.
The second run is usually much faster than a run with large scc
and bcc.

2. Metals

If you are doing a metal you should report the shift used in sigma.inp
whether using truncation or not.

3. Off-diagonal

If you are doing off-diagonal matrix elements of Sigma use the utility
offdiag in this directory to diagonalize the Sigma matrix.

4. Linear extrapolation for eqp1

If |eqp0 - ecor| > finite_difference_spacing linear extrapolation
for eqp1 may be inaccurate. You should test the validity of eqp1
by rerunning calculation with self-energy evaluated at the eqp0
energies. For that, use the eqp_outer.dat file created
with eqp.py script and point WFN_outer to WFN_inner (if you were
not already using WFN_outer), i.e. run
i) ln -s WFN_inner WFN_outer
ii) eqp.py eqp0 sigma_hp.log eqp_outer.dat
and add eqp_outer_corrections to sigma.inp. If you get the same eqp1,
the linearization looks good; if not, you can continue iterations like
this to converge to the solution of the Dyson equation.


## Sigma/sigma.inp

# sigma.inp

# G-vectors will be used with kinetic energies up to this cutoff (Ry)
# screened_coulomb_cutoff must be <= epsilon_cutoff used for Epsilon run
screened_coulomb_cutoff  8.0
bare_coulomb_cutoff      60.0

# number of bands to sum over
number_bands             146

# a list of which bands are occupied (1) and which are unoccupied (0)
band_occupation          18*1 128*0
# Note that what is above is Fortran shorthand for 18 1's and 128 0's.
# i.e. "4*1 4*0" is equivalent to "1 1 1 1 0 0 0 0"; either may be used here.

# If you have partially occupied bands (Metal) set
# number_partial_occup to the number of these bands.
# Set occupation of these bands to zero in the
# band_occupation line above.
# This is for bands that cross the Fermi energy, so
# that they are occupied at some k-points and not at
# others, rather than for thermal partial occupations.
# (this is former ncrit)
#number_partial_occup    0

# Specify the Fermi level (in eV), if you want implicit doping
# Note that value refers to energies AFTER scissor shift or eqp corrections.
#fermi_level             0.0

# The Fermi level is treated as an absolute value
# or relative to that found from the mean field (default)
#fermi_level_absolute
#fermi_level_relative

# The matrix elements of Sigma
# < psi_n | Sigma(E_l) | psi_m >
# E_l is irrelevant for frequency_dependence -1 and 0

# The diagonal matrix elements of Sigma (n .eq. m .eq. l)
#number_diag   ndiag
#begin diag
#   n_1
#   n_2
#   ...
#   n_ndiag
#end
# or specify a range of bands spanned by n
band_index_min   15
band_index_max   22

# The off-diagonal matrix elements of Sigma
# band_index_min .le. n .le. band_index_max
# band_index_min .le. m .le. band_index_max
# band_index_min .le. l .le. band_index_max
# NOTE: the offdiag utility only works with the sigma_matrix syntax, below.
#number_offdiag   noffdiag
#begin offdiag
#   n_1   m_1   l_1
#   n_2   m_2   l_2
#   ...
#   n_noffdiag   m_noffdiag   l_noffdiag
#end
# or select a specific value of l and let n and m vary
# in the range from band_index_min to band_index_max
# Set l to 0 to skip the off-diagonal calculation (default)
# If l = -1 then l_i is set to n_i (i = 1 ... noffdiag)
# i.e. each row is computed at different eigenvalue
# If l = -2 then l_i is set to m_i (i = 1 ... noffdiag)
# i.e. each column is computed at different eigenvalue
# For l > 0, all elements are computed at eigenvalue of band l.
# Set t to 0 for the full matrix (default)
# or to -1/+1 for the lower/upper triangle
#sigma_matrix   l   t

# The range of spin indices for which Sigma is calculated
# The default is the first spin component
#spin_index_min   1
#spin_index_max   1

# What screening is present? (default = semiconductor)
# Does not apply for frequency_dependence = -1.
screening_semiconductor
#screening_metal
#screening_graphene
#  this is for a system with linear DOS at the Fermi level

# RECOMMENDED fast FFTW truncation schemes
# The Coulomb Interaction is cutoff on the edges of
# the Wigner-Seitz Cell in the non-periodic directions
# Periodic directions are a1,a2 for slabs and a3 for wires

#cell_box_truncation
#cell_wire_truncation
#cell_slab_truncation

# Analytic, but non Wigner-Seitz cell, truncation

#spherical_truncation

# For Spherical Truncation, radius in Bohr

# Cutoff energy for averaging the Coulomb Interaction
# in the mini-Brillouin Zones around the Gamma-point
# without Truncation or for Cell Wire or Cell Slab Truncation.
# The value is in Rydbergs, the default is 10^{-12}
#cell_average_cutoff 1.0d-12

# Frequency dependence of the inverse dielectric matrix.
# Set to -1 for the Hartree-Fock approximation.
# Set to 0 for the static COHSEX approximation.
# Set to 1 for the Generalized Plasmon Pole model (default).
# Set to 2 for the full frequency dependence.
#frequency_dependence 1

# For Full Frequency Calculations.
# The number_frequency_eval is the number of frequency points
# to evaluate Sigma(omega) at.  The init_frequency_eval (eV)
# is the first frequency and delta_frequency_eval (eV) is the
# frequency step. The variable init_frequency_eval should be set
# relative to the Fermi energy (i.e., 0.0 means the Fermi energy)
# in case of frequency_dependence = 2, or relative to ecor
# (3rd column of sigma.log) in case of frequency_dependence = 1.
# These are NOT the values used in Epsilon for the evaluation of chi
# and epsilon - those are automatically read in from epsmat file.
#init_frequency_eval 0.0
#delta_frequency_eval 0.1
#number_frequency_eval 501

# For Generalized Plasmon Pole.
# The matrix element of the self-energy operator is
# expanded to first order in the energy around Ecor.
# Finite difference form for numerical derivative of Sigma.
# grid     = -3 : dSigma/dE = 0 Specify grid. Sigma.log will show value
#                 from second point. Spectrum.dat is more meaningful here.
# none     = -2 : dSigma/dE = 0 [skip the expansion].
# backward = -1 : dSigma/dE = (Sigma(Ecor) - Sigma(Ecor-dE)) / dE
# central  =  0 : dSigma/dE = (Sigma(Ecor+dE) - Sigma(Ecor-dE)) / (2*dE)
# forward  =  1 : dSigma/dE = (Sigma(Ecor+dE) - Sigma(Ecor)) / dE
# default  =  2 : forward for diagonal and none for off-diagonal
#finite_difference_form   2
# dE is finite difference spacing given in eV
# The default value is 1.0
#finite_difference_spacing   1.0

# For Hartree-Fock, no epsmat/eps0mat files are needed.
# Instead provide a list of q-points and the grid size.
# The list of q-points should not be reduced with time
# reversal symmetry - because BerkeleyGW never uses time
# reversal symmetry to unfold the q/k-points. Instead,
# inversion symmetry does the job in the real version of
# the code.
# qx qy qz 1/scale_factor is_q0
# scale_factor is for specifying values such as 1/3
# You can generate this list with kgrid.x: just set the shifts to zero and use
# same grid numbers as for WFN_inner. Then replace the zero vector with q0.
#number_qpoints  1
#begin qpoints
#  0.0  0.0  0.0  1.0  1
#end
#qgrid  1  1  1

# Summing SX and CH over G and G' vectors.
# Set to 1 for half sum (default) or 2 for full sum.
# Using 1 assumes W(G,G') = W(G',G) which should be
# satisfied in most situations. The only
# time you need to use 2 is if you are using a different
# Coulomb interaction (truncation scheme) between Epsilon
# and Sigma.  This is not really recommended anyway.
# If you are using no truncation, doing ggpsum = 1 is
# not exactly correct: W(G,G') will not be symmetric because
# we used an averaged V(0) in Sigma and a Non-Averaged V(q0)
# in Epsilon. This leads to errors on the order of 1 meV or less
# in examples.
# ggpsum 1 is (unintuitively) additionally slower than ggpsum 2
# do to poor load balancing with OpenMP and vectorization breakage.
# For these reasons ggpsum 2 will be made default in the future.
#ggpsum 1

# Add remainder from tail of epsilon for full frequency.
#use_epsilon_remainder

# Logging CH convergence.
# Set to 0 for the valence and conduction bands (default).
# Set to 1 for all bands, real part only.
# Set to 2 for all bands, real and imaginary parts.
# Note that CH in ch_converge.dat should be compared
# against unsymmetrized values in the standard output.
# This is different from sigma.log for degenerate states.
#full_ch_conv_log 0

# Use precalculated matrix elements of bare exchange from x.dat.
# The default is not to use them.
#use_xdat

# Do not use precalculated matrix elements of exchange-correlation from vxc.dat.
# The default is to use them.
#dont_use_vxcdat

# Relevant only if code is compiled with HDF5 support.
#dont_use_hdf5

# Fraction of bare exchange.
# Set to 1.0 if you use the exchange-correlation matrix elements
# read from file vxc.dat. Set to 1.0 for local density functional,
# 0.0 for HF, 0.75 for PBE0, 0.80 for B3LYP if you use the local
# part of the exchange-correlation potential read from file VXC.
# For functionals such as HSE whose nonlocal part is not some
# fraction of bare exchange, use vxc.dat and not this option.
# This is set to 1.0 by default.
#bare_exchange_fraction   1.0

# Broadening for the energy denominator in CH and SX within GPP.
# If it is less than this value, the sum is better conditioned than
# either CH or SX directly, and will be assigned to SX while CH = 0.
# This is given in eV, the default value is 0.5
# Cutoff for the poles in SX within GPP.
# Divergent contributions that are supposed to sum to zero are removed.
# This is dimensionless, the default value is 4.0
#gpp_sexcutoff   4.0

# kx ky kz 1/scale_factor
# scale_factor is for specifying values such as 1/3
number_kpoints   1
begin kpoints
0.0000  0.0000  0.0000  1.0
end

# Scissors operator (linear fit of the quasiparticle
# energy corrections) for the bands in WFN_inner
# e_cor = e_in + es + edel * (e_in - e0)
# Defaults below. evs, ev0, ecs, ec0 are in eV
#evs     0.0
#ev0     0.0
#evdel   0.0
#ecs     0.0
#ec0     0.0
#ecdel   0.0
# or
#cvfit   0.0 0.0 0.0 0.0 0.0 0.0

# Scissors operator (linear fit of the quasiparticle
# energy corrections) for the bands in WFN_outer
# e_cor = e_in + es + edel * (e_in - e0)
# Defaults below. evs_outer, ev0_outer, ecs_outer, ec0_outer are in eV
#evs_outer     0.0
#ev0_outer     0.0
#evdel_outer   0.0
#ecs_outer     0.0
#ec0_outer     0.0
#ecdel_outer   0.0
# or
#cvfit_outer   0.0 0.0 0.0 0.0 0.0 0.0

# Set this to use eigenvalues in eqp.dat
# If not set, this file will be ignored.
#eqp_corrections
# Set this to use eigenvalues in eqp_outer.dat
# If not set, this file will be ignored.
#eqp_outer_corrections

# The average potential on the faces of the unit cell
# in the non-periodic directions for the bands in WFN_inner
# This is used to correct for the vacuum level
# The default is zero, avgpot is in eV
#avgpot   0.0

# The average potential on the faces of the unit cell
# in the non-periodic directions for the bands in WFN_outer
# This is used to correct for the vacuum level
# The default is zero, avgpot_outer is in eV
#avgpot_outer   0.0

# Write the bare Coulomb potential V(q+G) to file
#write_vcoul

# Communication through MPI or DISK
# comm_mpi is usually much faster and preferable but if you have only
# a few CPUs you might not have enough memory to hold wavefunctions
# comm_disk results in temporary INT_* files being created and it
# may be faster for a small unit cell and a lot of k-points
# The default is comm_mpi.
comm_mpi
#comm_disk

# Number of pools for parallel sigma calculations
# The default is chosen to minimize memory in calculation
#number_sigma_pools 1

# Threshold for considering bands degenerate, for purpose of
# band-averaging and setting offdiagonals to zero by symmetry. (eV)
tol_degeneracy 1e-6

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY
# 'unfolded BZ' is from the kpoints in the WFN_inner file
# 'full BZ' is generated from the kgrid parameters in the WFN_inner file
# See comments in Common/checkbz.f90 for more details
# Replace unfolded BZ with full BZ
#fullbz_replace
# Write unfolded BZ and full BZ to files
#fullbz_write

# The requested number of bands cannot break degenerate subspace
# Use the following keyword to suppress this check
# Note that you must still provide one more band in
# wavefunction file in order to assess degeneracy
#degeneracy_check_override

# The sum over q-points runs over the full Brillouin zone.
# For diagonal matrix elements between non-degenerate bands
# and for spherically symmetric Coulomb potential (no truncation
# or spherical truncation), the sum over q-points runs over
# the irreducible wedge folded with the symmetries of
# a subgroup of the k-point. The latter is the default.
# In both cases, WFN_inner should have the reduced k-points
# from an unshifted grid, i.e. same as q-points in Epsilon.
# With no_symmetries_q_grid, any calculation can be done;
# use_symmetries_q_grid is faster but only diagonal matrix elements
# of non-degenerate or band-averaged states can be done.
#no_symmetries_q_grid
#use_symmetries_q_grid

# Off-diagonal elements are zero if the two states belong to
# different irreducible representations. As a simple proxy,
# we use the size of the degenerate subspaces of the two states:
# if the sizes are different, the irreps are different, and the
# matrix element is set to zero without calculation.
# Turn off this behavior for testing by setting flag below.
# Using WFN_outer effectively sets no_symmetries_offdiagonals.
#no_symmetries_offdiagonals

# Rotation of the k-points may bring G-vectors outside of the sphere.
# Use the following keywords to specify whether to die if some of
# the G-vectors fall outside of the sphere. The default is to die.
# Set to die in case screened_coulomb_cutoff = epsilon_cutoff.
# Set to ignore in case screened_coulomb_cutoff < epsilon_cutoff.
#die_outside_sphere
#ignore_outside_sphere

# Dealing with the convergence of the CH term.
# Set to 0 to compute a partial sum over empty bands.
# Set to 1 to compute the exact static CH.
# In case of exact_static_ch = 1 and frequency_dependence = 1 (GPP) or 2 (FF),
# the partial sum over empty bands is corrected with the static remainder
# which is equal to 1/2 * (exact static CH - partial sum static CH),
# additional columns in sigma_hp.log labeled ch', sig', eqp0', eqp1'
# are computed with the partial sum without the static remainder,
# and ch_converge.dat contains the static limit of the partial sum.
# In case of exact_static_ch = 0 and frequency_dependence = 0 (COHSEX),
# columns ch, sig, eqp0, eqp1 contain the exact static CH,
# columns ch', sig', eqp0', eqp1' contain the partial sum static CH,
# and ch_converge.dat contains the static limit of the partial sum.
# For exact_static_ch = 1 and frequency_dependence = 0 (COHSEX),
# columns ch', sig', eqp0', eqp1' are not printed and
# file ch_converge.dat is not written.
# Default is 0 for frequency_dependence = 1 and 2;
# 1 for frequency_dependence = 0;
# has no effect for frequency_dependence  = -1.
#
# It is important to note that the exact static CH answer
# depends not only on the screened Coulomb cutoff but also on the bare Coulomb cutoff
# because G-G' for G's within the screened Coulomb cutoff can be outside the screened
# Coulomb cutoff sphere. And, therefore, the bare Coulomb cutoff sphere is used.
#exact_static_ch 0

# Do not average W over the minibz, and do not replace the head of eps0mat with
# averaged value.
#skip_averagew


## Sigma/sig2wan.inp

sigma_hp.log   ! Sigma output file to read k-points, eigenvalues and symmetries from
1            ! spin component to read from sigma_hp.log file
1            ! set to 0 or 1 to read eqp0 or eqp1 from sigma_hp.log file
prefix.nnkp  ! Wannier90 input file to read k-points from
prefix.eig   ! file where the output of sig2wan is written
nbands       ! number of bands to write out


## BSE

-----------------------------------------------------------------
----------  BSE code, Kernel  -----------------------------------
-----------------------------------------------------------------

Version 1.1   (June, 2014)

Version 1.0	(July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze.
Version 0.5	J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008)
Version 0.2	C. Spataru, S. Ismail-Beigi (2004)
Version 0.1	M. L. Tiago, E. Chang, G. M. Rignanese (1999)

-----------------------------------------------------------------

Description:

This code constructs the direct and exchange Kernel matrix on
the coarse grid.  This is done essentially by computing Eqs 34,
35 and 42-46 of Rohlfing and Louie.

-----------------------------------------------------------------

Required Input:

kernel.inp	Input parameters.  See detailed explanation below.
WFN_co		Wavefunctions on coarse grid. Recommended: use an unshifted
grid of the same size as the q-grid in epsmat.
Shift will increase number of q-vectors needed in epsmat.

epsmat		Inverse dielectric matrix (q<>0).  Created using Epsilon.
Must contain the all q=k-k' generated from WFN_co, including
with symmetry if use_symmetries_coarse_grid is set.
eps0mat		Inverse dielectric matrix (q->0).  Created using Epsilon.

Note Kernel does not require quasiparticle eigenvalues. It
may be run in parallel with Sigma.

-----------------------------------------------------------------

kernel.inp	Please see example kernel.inp in this directory
for more complete options.

-----------------------------------------------------------------

Output Files:

bsedmat		Direct kernel matrix elements on unshifted coarse grid.
bsexmat		Exchange kernel matrix elements on unshifted coarse grid.

or

bsemat.h5	Includes data from both of above if compiled with HDF5 support
For specification, see bsemat.h5.spec

-----------------------------------------------------------------

A Note About the Wings of Epsilon (for Semiconductors Only):

The wings of Chi have terms of the following form:

< vk | e^(i(G+q)r) | ck+q >< ck+q | e^(-iqr) | vk > (1)

The matrix element on the right is < u_ck+q | u_vk > where u is the periodic part
of the Bloch function. From k.p perturbation theory, this matrix element is proportional
to q. The matrix element on the left with a non-zero G is typically roughly
a constant as a function of q for small q (q being a small addition to G).

Thus for a general G-vector, Chi_wing(G,q) \propto q. This directly leads
to the wings of the screened untruncated Coulomb interaction being proportional
to 1/q. Note that this function changes sign as q -> -q. Thus, when treating the
q=0 point, we set the value of the wing to zero (the average of its value in the
mini-Brillouin zone (mBZ).

For G-vectors on high-symmetry lines, some of the matrix elements on the left of (1)
will be zero for q=0, and therefore proportional to q. For such cases,
Chi_wing(G,q) \propto q^2, and the wings of the screened Coulomb interaction
are constant as a function of q. However, setting the q->0 wings to zero still
gives us, at worst, linear convergence to the final answer with increased k-point
sampling, because the q->0 point represents an increasingly smaller area in the
BZ. Thus, we still zero out the q->0 wings, as discussed in
A Baldereschi and E Tosatti, Phys. Rev. B 17, 4710 (1978).

In the future, it may be worthwhile to have the user calculate chi / epsilon at
two q-points (a third q-point at q=0 is known) in order to compute the linear
and quadratic coefficients of each chi_wing(G,q) so that all the correct analytic
limits can be taken. This requires a lot of messy code and more work for the user
for only marginally better convergence with respect to k-points (the wings tend
to make a small difference, and this procedure would matter for only a small set
of the G-vectors).

It is important, as always, for the user to converge their calculation
with respect to both the coarse k-point grid used in sigma and kernel as well
as with the fine k-point grid in absorption.

-JRD+MJ

-----------------------------------------------------------------

Tricks and hints:

1. To optimize distribution of work among PEs, do the following:

Choose processors to divide:

nk^2 (if npes < nk^2)
nk^2*nc^2 (if npes < nk^2*nc^2)
nk^2*nc^2*nv^2 (if npes < nk^2*nc^2*nv^2)

2. All input and output files (except kernel.inp) are in
binary format.

3. The interaction matrices are calculated in full! i.e. not only the
upper triangle. In diag, currently only the upper triangle is used.

4. The Brillouin zone is built using a Wigner-Seitz construction,
this way the head matrix elements are easily calculated.

5. The dielectric matrix is by default stored in memory but may be stored
on disk if the comm_disk options is specified.

6. The parameters scc (screened_coulomb_cutoff) and bcc
(bare_coulomb_cutoff) are the same as scc and bcc used in Simga.
The parameters scc and bcc should be equal to or less than the
epsilon_cutoff and wavefunction_cutoff used in Epsilon and DFT,
respectively. See Sigma/README for more details.

Converters from old versions of file formats to current version are available in version 2.4.


## BSE/kernel.inp

# kernel.inp

# specify the number of valence bands (counting down from HOMO)
number_val_bands 3

# conduction bands (counting up from LUMO)
number_cond_bands 3

# screened coulomb cutoff (Ry) - must be specified as non-zero
# ecute in the code
screened_coulomb_cutoff 8.0

# bare coulomb cutoff (Ry) - if not specified set to ecute + max(bdot)
# ecutg in the code
bare_coulomb_cutoff 60.0

# Specify the Fermi level (in eV), if you want implicit doping
# Note that value refers to energies AFTER scissor shift or eqp corrections.
#fermi_level 0.0

# The Fermi level is treated as an absolute value
# or relative to that found from the mean field (default)
#fermi_level_absolute
#fermi_level_relative

# What screening is present? (default = semiconductor)
screening_semiconductor
#screening_metal
#screening_graphene
#  this is for a system with linear DOS at the Fermi level

# RECOMMENDED fast FFTW truncation schemes
# The Coulomb Interaction is cutoff on the edges of
# the Wigner-Seitz Cell in the non-periodic directions
# Periodic directions are a1,a2 for slabs and a3 for wires

#cell_box_truncation
#cell_wire_truncation
#cell_slab_truncation

# Analytic, but non Wigner-Seitz cell, truncation

#spherical_truncation

# For Spherical Truncation, radius in Bohr

# Flag for coarse grid of k-points in the BZ.
# Should we unfold using symmetries? either
# no_symmetries_coarse_grid (default) or
# use_symmetries_coarse_grid. If you calculated
# epsmat on a reduced q grid, you should use
# symmetries here!
#use_symmetries_coarse_grid
no_symmetries_coarse_grid

# Write the bare Coulomb potential V(q+G) to file
#write_vcoul

# Communication through MPI or DISK
# comm_mpi is usually much faster and preferable but if you have only
# a few CPUs you might not have enough memory to hold wavefunctions
# comm_disk results in temporary INT_* files being created and it
# may be faster for a small unit cell and a lot of k-points
# The default is comm_mpi
# *** CURRENTLY, comm_disk IS ONLY IMPLEMENTED FOR eps0mat/epsmat ***
comm_mpi
#comm_disk

# Low communication
# The default behavior of the code is to distribute the dielectric matrix
# among the processors. While this minimizes memory usage, it also
# increases the communication. By using the low_comm flag, each processor
# will store the whole dielectric matrix. It is advisable to use this flag
# whenever each PE has enough memory to hold the whole epsmat file.
#low_comm

# Low Memory option
# Calculate matrix elements separately for each k,c,v,k',c',v' pair
#low_memory

# Use traditional simple binary format for bsedmat/bsexmat instead of HDF5 file format.
# Relevant only if code is compiled with HDF5 support.
#dont_use_hdf5

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY
# High Memory option
# Save all wavefunction FFTs when calculating the BSE kernel.
# Overwrites the low_memory option.
#high_memory

# 'unfolded BZ' is from the kpoints in the WFN file
# 'full BZ' is generated from the kgrid parameters in the WFN file
# See comments in Common/checkbz.f90 for more details
# Replace unfolded BZ with full BZ
#fullbz_replace
# Write unfolded BZ and full BZ to files
#fullbz_write

# Rotation of the k-points may bring G-vectors outside of the sphere.
# Use the following keywords to specify whether to die if some of
# the G-vectors fall outside of the sphere. The default is to ignore.
# Set to die in case screened_coulomb_cutoff = bare_coulomb_cutoff.
# Set to ignore in case screened_coulomb_cutoff < bare_coulomb_cutoff.
#die_outside_sphere
#ignore_outside_sphere

# Flag to read k-points from the 'kpoints' file.
# The default is to read k-points from the wfn file.



-----------------------------------------------------------------
----------  BSE code, Absorption  -------------------------------
-----------------------------------------------------------------

Version 1.1   (June, 2014)

Version 1.0	(July, 2011) J. Deslippe, M. Jain, D. A. Strubbe, G. Samsonidze
Version 0.5	J. Deslippe, D. Prendergast, L. Yang, F. Ribeiro, G. Samsonidze (2008)
Version 0.2	M. L. Tiago, C. Spataru, S. Ismail-Beigi (2004)

-----------------------------------------------------------------

Description:

This code is the second half of the BSE code.  It interpolates the coarse grid
electron-hole kernel onto the fine grid and then diagonalized the BSE equation.
The output is the electron-hole eigenfunctions and eigenvalues as well the
absorption spectra.

-----------------------------------------------------------------

Required Input:

absorption.inp	Input parameters.  See detailed explanation below.
WFN_fi		Wavefunctions in unshifted fine grid
(conduction and valence for momentum operator,
conduction for velocity operator).
WFNq_fi		Wavefunctions in shifted fine grid
(not needed for momentum operator,
valence for velocity operator).
WFN_co		Wavefunctions on unshifted coarse grid.
Must be the same as used for Kernel.
eps0mat		Must be same as used in Kernel.
epsmat		Must be same as used in Kernel.
bsedmat		BSE matrix elements in coarse grid, direct part. This
should be generated with Kernel code using same WFN_co.
bsexmat		BSE exchange matrix elements.  This should be generated
with Kernel code using same WFN_co.

eqp.dat		A list of quasiparticle energy corrections for the bands in WFN_fi.
Used if eqp_corrections is set in absorption.inp.
eqp_q.dat	A list of quasiparticle energy corrections for the bands in WFNq_fi.
Used if eqp_corrections is set in absorption.inp.
eqp_co.dat	A list of quasiparticle energy corrections for the bands in WFN_co.
Used if eqp_co_corrections is set in absorption.inp.

kpoints		A list of k-points in unshifted fine grid. EXPERIMENTAL.
If absent k-points from WFN_fi file are used.
kpoints_co	A list of k-points in unshifted coarse grid. EXPERIMENTAL.
If absent k-points from WFN_co file are used.

Auxiliary Files: (output files from previous runs - used as input to speed up calculation)

dtmat		Transformation matrices, dcc/dvv use for interpolation
between coarse and fine grid.  This file must be consistent
with your bsedmat and bsexmat files and corresponding
coarse and fine wavefunctions.
NOTE: the file format for dtmat was changed in BerkeleyGW 1.1.0	(r5961)
vmtxel		Optical matrix elements (velocity or momentum) between
single particle states.
epsdiag.dat	Diagonal elements of dielectric matrix on the q-grid.
Must be consistent with epsmat and eps0mat.
eigenvalues.dat	Contains electron-hole eigenvalues and transition matrix elements.

-----------------------------------------------------------------

absorption.inp	Please see example absorption.inp in this directory
for more complete options.

-----------------------------------------------------------------

Output Files:

eigenvalues.dat	  	Has eigenvalues/transition matrix elements of e-h states,
eigenvalues in eV, mtxels in atomic units.
eigenvectors	  	Has the excitonic wavefunctions in Bloch space:
A_svck
absorption_eh.dat	Dielectric function and density of excitonic states.
Four Columns
energy (in eV) | epsilon_2 | epsilon_1 | DOS
DOS is normalized (\int (DOS) d(omega) = 1)
absorption_noeh.dat	Non-interacting dielectric function and joint density
of states.  Four columns:
energy (in eV) | epsilon_2 | epsilon_1 | JDOS
JDOS is normalized (\int (JDOS) d(omega) = 1)
dvmat_norm.dat		The norms of the dvv overlap matrices between the valence
band k on the fine grid and the closest k-point on the coarse grid
dcmat_norm.dat		The norms of the dcc overlap matrices between the conduction
band k on the fine grid and the closest k-point on the coarse grid
eqp.dat, eqp_q.dat      Quasiparticle corrections for WFN_fi and WFNq_fi interpolate from
the coarse grid if eqp_co_corrections is used.
bandstructure.dat       Same as eqp.dat and eqp_q.dat but in a format suitable for plotting
as a bandstructure.

-----------------------------------------------------------------

Tricks and hints:

1. To optimize distribution of work among PEs, choose the number of
PEs so that Nk*Nc*Nv in the fine grid is a multiple of the
number of PEs. The parallelization is first done over over k-points.

2. The Brillouin zone is built using a Wigner-Seitz construction,
this way the head matrix elements are easily calculated.

3. Check if the transformation matrices have norm close to 1! They
are usually normalized (look at the end of intwfn.f90). The norms are in
the files dvmat_norm.dat and dcmat_norm.dat.

4. Unfolding of irreducible BZ: if you want to skip the unfolding and
use the set of k-points in WFN_fi as a sampling of the whole BZ, specify
the no_symmetries_* options in absorption.inp.

5. The "number_eigenvalues" keyword: using this keyword tells the code
to store only the first nn eigenvalues/eigenvectors. So far, this option
is implemented only with the SCALAPACK diagonalization routines.

6.  Analyzing eigenvectors.  We have a tool called summarize_eigenvectors to read in
and analyze eigenvectors for a group of exciton states.  For specific states
specified, it sums the total contribution from each k-point.
Please see the example input summarize_eigenvectors.inp.

Converters from old versions of file formats to current version are available in version 2.4.


## BSE/absorption.inp

# absorption.inp

##########################################
# OPTIONS FOR BOTH ABSORPTION AND INTEQP #
##########################################

# Number of occupied bands on fine (interpolated) k-point grid
number_val_bands_fine 3
# Number of occupied bands on coarse (input) k-point grid
number_val_bands_coarse 3

# Number of unoccupied bands on fine (interpolated) k-point grid
number_cond_bands_fine 3
# Number of unoccupied bands on coarse (input) k-point grid
number_cond_bands_coarse 3

# In metallic systems, PARATEC often outputs incorrect occupation
# levels in wavefunctions.  Use this to override these values.
# lowest_occupied_band should be 1 unless you have some very
# exotic situation.
#lowest_occupied_band vmin
#highest_occupied_band vmax

# Specify the Fermi level (in eV), if you want implicit doping
# Note that value refers to energies AFTER scissor shift or eqp corrections.
# If the Fermi level is moved, then you must use both or neither
# of eqp_corrections and eqp_co_corrections, or no interpolation.
# NOTE: If you are using inteqp.x to interpolate eqp_co.dat into a eqp.dat
# file that will be later used in absorption.x, shift the Fermi level only
# in absorption.x, but not in inteqp.x.
#fermi_level 0.0

# The Fermi level is treated as an absolute value
# or relative to that found from the mean field (default)
#fermi_level_absolute
#fermi_level_relative

# Scissors operator (linear fit of the quasiparticle
# energy corrections) for the bands in WFN_fi and WFNq_fi.
# e_cor = e_in + es + edel * (e_in - e0)
# Defaults below. evs, ev0, ecs, ec0 are in eV
#evs     0.0
#ev0     0.0
#evdel   0.0
#ecs     0.0
#ec0     0.0
#ecdel   0.0
# or
#cvfit   0.0 0.0 0.0 0.0 0.0 0.0

# These flags define whether to use symmetries to unfold
# the Brillouin zone or not in files WFN_fi (unshifted fine
# grid), WFNq_fi (shifted fine grid), WFN_co (coarse grid).
# Warning, the default is always not to unfold!

# If your unshifted fine grid is reduced (most cases),
# you will want to use symmetries here!
#no_symmetries_fine_grid
#use_symmetries_fine_grid

# If your shifted fine grid is reduced (most cases),
# you will want to use symmetries here! Note that
# if you use symmetries in the unshifted grid you will
# need to generate the shifted grid using the same
# procedure as generating the shifted grid for an
# epsilon calculation. i.e. use gw_shift in paratec
# and a non-zero small q-shift in kgrid.inp
#no_symmetries_shifted_grid
#use_symmetries_shifted_grid

# If you calculated the coarse grid on a reduced q-grid,
# you should use symmetries here!
#no_symmetries_coarse_grid
#use_symmetries_coarse_grid

# Regular grid used to calculate qpt_averages.
# Default is the kgrid in the WFN_fi file.
# It matters only if you want to perform minicell averages.
#regular_grid n1 n2 n3

# How to calculate optical transition probabilities.
# No default for absorption, one must be specified.
# For inteqp, default is momentum.
# For momentum and JDOS, only WFN_fi is used.
# For velocity, the valence bands come from WFNq_fi.
use_velocity
#use_momentum
# For Haydock there is also a third option to calculate
#use_dos

# Communication through MPI or DISK
# comm_mpi is usually much faster and preferable but if you have only
# a few CPUs you might not have enough memory to hold wavefunctions
# comm_disk results in temporary INT_* files being created and it
# may be faster for a small unit cell and a lot of k-points.
# The default is comm_mpi
# *** Code often crashes in genwf_co with comm_disk when run on ***
# *** a large number of processors because all instances are trying to ***
# *** read coarse grid wavefunctions simultaneously from a single INT file ***
comm_mpi
#comm_disk

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY (ABSORPTION AND INTEQP)
# 'unfolded BZ' is from the kpoints in the WFN file
# 'full BZ' is generated from the kgrid parameters in the WFN file
# See comments in Common/checkbz.f90 for more details
# Replace unfolded BZ with full BZ
#fullbz_replace
# Write unfolded BZ and full BZ to files
#fullbz_write

# Flag to read k-points from the 'kpoints' file.
# The default is to read k-points from the wfn file.

# This is needed only with read_kpoints and if you selected velocity operator above.
# This should match the shift between WFN_fi and WFNq_fi.
q_shift s1 s2 s3

# The requested number of valence or conduction bands cannot break degenerate subspace.
# Use the following keyword to suppress this check.
# Note that you must still provide one more band in
# wavefunction file in order to assess degeneracy.
# For inteqp, only the coarse grid is checked.
#degeneracy_check_override

#####################################
# OPTIONS ONLY FOR ABSORPTION BELOW #
#####################################

# Whether to do a diagonalization (with ScaLAPACK or LAPACK) or
# an iterative solution (via Haydock Recursion).
# diagonalization is default

diagonalization
#haydock

# What screening is present? (default = semiconductor)
screening_semiconductor
#screening_metal
#screening_graphene
#  this is for a system with linear DOS at the Fermi level

# Compute only the lowest neig eigenvalues/eigenvectors.
# The default is to calculate all nv*nc*nk of them.
# Only for diagonalization, not for haydock.
#number_eigenvalues neig

# If using Haydock specify the number of iterations
#number_iterations 500

# Set this to use eigenvalues in eqp.dat and eqp_q.dat
# If not set, these files will be ignored.
#eqp_corrections

# Set this to use eigenvalues in eqp_co.dat
# These quasiparticle corrections will be interpolated to
# the shifted and unshifted fine grids and written to eqp.dat,
# eqp_q.dat, and bandstructure.dat. If not set, this file will be ignored.
#eqp_co_corrections

# RECOMMENDED fast FFTW truncation schemes
# The Coulomb Interaction is cutoff on the edges of
# the Wigner-Seitz Cell in the non-periodic directions
# Periodic directions are a1,a2 for slabs and a3 for wires

#cell_box_truncation
#cell_wire_truncation
#cell_slab_truncation

# Analytic, but non Wigner-Seitz cell, truncation

#spherical_truncation

# For Spherical Truncation

# Cutoff energy for averaging the Coulomb Interaction
# in the Mini Brillouin Zones around the Gamma-point
# without Truncation or for Cell Wire or Cell Slab Truncation.
# The value is in Rydbergs, the default is 10^{-12}
#cell_average_cutoff 1.0d-12

# This is needed if you selected momentum operator above.
# This vector will be normalized in the code.
#polarization p1 p2 p3

# If we have already calculated the optical matrix elements,
# do we read them from file to save time?

# Read 'eps2_moments' generated during previous run (Haydock only)

# Reduce cost of calculation if we've already computed
# the eigensolutions.  This reads the eigenvalues and
# transition matrix elemenents from the file 'eigenvalues.dat'

# If we only want the noninteracting spectra (i.e. no electron-
# hole interaction).  Only WFN_fi and WFNq_fi are needed as inputs.
# With the 'read_eigenvalues' flag, both absorption_eh.dat and
# absorption_noeh.dat will be created.
#noeh_only

# and dcc from file dtmat.

# Numerical broadening width and type for generating absorption spectrum.
# Haydock only does Lorentzian. epsilon_1 is always Lorentzian.
# The width is controlled by energy_resolution.
energy_resolution 0.1
# epsilon_2 with diagonalization is Gaussian by default. You can also choose Lorentzian.

# The Gaussian and Voigt options are only available for epsilon_2 with diagonalization.
# Voigt becomes Lorentzian at sigma -> 0 and Gaussian at gamma = 0.
# Note that the parametrization of Voigt function diverges at sigma = 0.
#energy_resolution_sigma 0.1
#energy_resolution_gamma 0.01

# This specifies what kind of epsilon we read.
# Default is to read epsmat and eps0mat, but if
# epsdiag.dat contains only the diagonal part of eps(0)mat
# which is all that is needed by absorption. It is always created
# by an absorption run for use in future runs, to save time reading.

# Determines output of eigenvectors (eigenvectors)
# eig = 0 : do not write eigenvectors (default)
# eig < 0 : write all eigenvectors
# eig > 0 : write eig eigenvectors
#write_eigenvectors eig

# Flag the type of kernel to calculate:
# spin_triplet: direct kernel only (no exchange).
#  WARNING: triplet transition matrix elements would be exactly for electric-dipole transitions,
#  so we give instead the spin part of magnetic-dipole interaction.
# spin_singlet (default): direct + exchange. appropriate for spin-polarized too.
# local_fields: local-fields + RPA (exchange only)
# Note that triplet kernel only applies to a spin-unpolarized system;
# for a spin-polarized system, the solutions naturally include both singlets and triplets
# (or other multiplicities for a magnetic system).
#spin_triplet
#spin_singlet
#local_fields

# Write the bare Coulomb potential V(q+G) to file
#write_vcoul

# If your two grids are the same, use this flag to skip interpolation and
# reduce the time/memory you need. DO NOT use this if you have a different
# fine grid from the coarse grid, as for velocity operator.
# Then you should use eqp_corrections with eqp.dat (and eqp_q.dat).
#skip_interpolation

# The new interpolation algorithm is based on the Delaunay tessellation of the
# k-points. This guarantees that the interpolant is a continuous function, and
# that we are always interpolating, and never extrapolating. (default)
#delaunay_interpolation
# You can also use the previous interpolation method, which might give
# interpolants that are not continuous.
#greedy_interpolation

# Relevant only if code is compiled with HDF5 support.
#dont_use_hdf5

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY (ABSORPTION ONLY)

# for the inverse dielectric matrix. This is done for insulators for
# all truncation schemes. The W average is limited only to the first
# minibz even if cell_average_cutoff != 0. Currently it is always done
# regardless whether average_w is included in the input file or not.
#average_w

# Multiply kernel by arbitrary factor. Default is 1.0 of course.
kernel_scaling 1.0



## BSE/inteqp.inp

# inteqp.inp
# inteqp.inp uses a subset of the parameters from absorption.inp
# Please see absorption.inp for examples.


-----------------------------------------------------------------
----------  BSE code, IntEqp  -----------------------------------
-----------------------------------------------------------------

Version 1.0	(July, 2011) J. Deslippe, D. A. Strubbe

-----------------------------------------------------------------

Description:

This code takes the eqp_co.dat file from Sigma and
interpolates it from the coarse to the fine grid using wavefunction
projections (to resolve band crossings) and linear interpolation
in the Brillouin zone.

-----------------------------------------------------------------

Required Input:

inteqp.inp	Input parameters. See example absorption.inp in this directory
for complete options (noting which sections apply to inteqp).
WFN_fi		Wavefunctions in unshifted fine grid.
WFN_co		Wavefunctions on coarse grid.
eqp_co.dat	A list of quasiparticle energy corrections
for the bands in WFN_co.

Optional Input:

WFNq_fi         Wavefunctions in shifted fine grid
(used for valence bands if use_velocity is selected)

Auxiliary Files: (output files from previous runs - used as input to speed up calculation)

dtmat		Transformation matrices, dcc/dvv use for interpolation
between coarse and fine grid.  This file must be consistent
with your bsedmat and bsexmat files and corresponding
coarse and fine wavefunctions.
NOTE: the file format for dtmat was changed in BerkeleyGW 1.1.0	(r5961)

-----------------------------------------------------------------

Output Files:

bandstructure.dat	The GW bandstructure on the fine grid.
eqp.dat                 Quasiparticle energy corrections for the bands in WFN_fi.
eqp_q.dat               Quasiparticle energy corrections for the bands in WFNq_fi (if use_velocity).
dvmat_norm.dat		The norms of the dvv overlap matrices between the valence
band k on the fine grid and the closest k-point on the coarse grid
dcmat_norm.dat		The norms of the dcc overlap matrices between the conduction
band k on the fine grid and the closest k-point on the coarse grid


## BSE/summarize_eigenvectors.inp

20		! Number of eigenvectors in file.  Set to zero to use default ns*nv*nc*nk
1.5 2.1  	! Emin Emax (eV). Energy window to print information about all states in
3        	! Number of specific states to print A(k). Output files will be exciton_01 ... exciton_99
1.56783332	! Energy values (eV) of the states to print A(k)
1.67345203
1.96328918


## PlotXct

-----------------------------------------------------------------
----------  PlotXct code  ---------------------------------------
-----------------------------------------------------------------

Version 1.1   (June, 2014)

Version 1.0	(July, 2011)

Version 0.5	F. Ribeiro (2008), S. Ismail-Beigi
Version 0.2	M. L. Tiago (2002-2007)

-----------------------------------------------------------------

Description:

PlotXct plots the exciton wavefunction in real space based on
output of BSE/absorption (with full diagonalization).

Reads files WFN_fi/WFNq_fi (from mean field) and eigenvectors (output
from BSE/absorption code when using diagonalization, not Haydock) and
plots selected exciton state in real space according to:

Psi(r,r,s) = Sum_cvk A_svck * phi_sck(r) * exp(ik.r) * conjg( phi_svk(r) * exp(i[k+q].r)

where r, hole coordinate, is fixed at some point and r, electron coordinate,
runs over a supercell of given size (typically, equivalent to the fine k-grid),
with a real-space mesh defined by the FFT grid of the wavefunction files.
A separate plot can be generated for each spin s.

Output is written in format suitable for Data Explorer (DX).

The input option 'restrict_kpoints' reduces the sum over k-points
above to a sum over the ones that give most of the contribution
to the norm of eigenvectors. This is handy if there are many k-points
but only a few of them give sizable contribution.

input: WFN_fi WFNq_fi       wavefunction files
eigenvectors         output from BSE/absorption code
plotxct.inp          input parameters

-----------------------------------------------------------------

1. Copy/edit plotxct.inp.

You'll need:
. index of the exciton state you want to plot
. hole position in lattice coordinates
. supercell dimensions (or k-grid)
. spin component you want to plot (if spin-polarized)

2. Run plotxct.x

The ASCII file 'xct.[state]_s[spin].a3Dr' will be created.

'a3Dr' means that the file is in ASCII and contains 3D data in 'r' real space.

The header of this file contains information on
. state index
. state energy in eV
. hole position in atomic units (a.u.)
. spin component plotted
. supercell lattice vectors in a.u.
. number of discretization points
followed by three columns of data corresponding to the complex values of the
electronic part of the excitonic wavefunction, and its magnitude squared.

The values are written with very low precision due to file-size concerns.

3. Convert to a format readable by the plotting utility of your choice.

Use the 'volume.py' utility:

Usage: volume.py imfn imff ivfn ivff ovfn ovff phas cplx [hole]

imfn = input matter file name
imff = input matter file format
(mat|paratec|vasp|espresso|siesta|tbpw|xyz|xsf)
ivfn = input volumetric file name
ivff = input volumetric file format (a3dr)
ovfn = output volumetric file name
ovff = output volumetric file format (cube|xsf)
phas = remove wavefunction phase (true|false)
cplx = complex wavefunction (re|im|abs|abs2)
hole = plot hole (true|false)

You can specify whether you want a .xsf (XCrysDen) or .cube (Gaussian Cube)
file format. You can remove or keep the arbitrary phase of the wavefunction
by setting parameter "phas" to true or false. You can plot the re, im, abs,
or abs2 part of the wavefunction.

You must specify a path to the input file (example: "../01-scf/input")
in one of the supported formats (DFT and others) so that the script can
obtain the atomic positions from the file.

You can choose whether to display or not the position of the hole by setting
parameter "hole" to true or false.

The resulting .xsf or .cube file can be viewed in XCrysDen or converted to
POV-Ray script format using Surface code (for more details on the latter

****************
Example:

% ~/BerkeleyGW/Visual/volume.py ../01-scf/input paratec xct.000001_s1.a3Dr a3dr \
xct.000001.abs2.xsf xsf false abs2 false
% xcrysden --xsf xct.000001.abs2.xsf

****************


## PlotXct/plotxct.inp

#
# Index of state to be plotted, as it appears in eigenvectors
#
plot_state 20

#
# Index of spin component of the exciton to plot. Default is 1.
#
plot_spin 1

#
# Size of supercell
#
supercell_size 1 1 60

#
# coordinates of hole, in units of lattice vectors
# (usually, hole in the center of the supercell)
#
hole_position    0.8025    0.3487    30.00
# corresponds to  21.121073141660   22.792380000000   0.005915241051  in real space + 50*(0,0,az)
# hole 2 a.u. on x dir from an atom at 5.96137532  0.0 from center of tube
# original coord:     19.121073141660   22.792380000000    0.005915241051
#

# input option 'restrict_kpoints' reduces the sum over k-points
# above to a sum over the specified number that give most of the contribution
# to the norm of eigenvectors. This is handy if there are many k-points
# but only a few of them give sizable contribution.
#restrict_kpoints 5

#  q-shift used in the calculation of valence bands (WFNq_fi file)
# Only needed if restrict_kpoints is used, otherwise determined automatically.
q_shift   0.00000  0.00000  0.00000

# EXPERIMENTAL FEATURES FOR TESTING PURPOSES ONLY
# 'unfolded BZ' is from the kpoints in the WFN file
# 'full BZ' is generated from the kgrid parameters in the WFN file
# See comments in Common/checkbz.f90 for more details
# Replace unfolded BZ with full BZ
#fullbz_replace
# Write unfolded BZ and full BZ to files
#fullbz_write



## Visual

-----------------------------------------------------------------
----------  Visualization Tools  --------------------------------
-----------------------------------------------------------------

Version 2.4	(May, 2009)

Version 2.3	G. Samsonidze (October, 2008)

-----------------------------------------------------------------

Description:

This directory contains a set of visualization tools designed to
simplify your work with the DFT codes and the BerkeleyGW package.
Here you will find the following scripts and codes:

1. Surface is a C++ code for generating an isosurface of a volumetric
scalar field (such as the wave function, charge density, or local
potential). The scalar field is read from Gaussian Cube or XCrySDen
XSF file, the surface triangulation is performed using marching cubes
or marching tetrahedra algorithm, and the isosurface is written in
the POV-Ray scripting language. The final image is rendered using
the ray-tracing program POV-Ray.

Running the code requires a fairly complicated input parameter file,
described with an example in surface.inp.

2. Matter is a python library for manipulating atomic structures with
periodic boundary conditions. It can translate and rotate the atomic
coordinates, generate supercells, assemble atomic systems from fragments,
and convert between different file formats. The supported file formats
are mat, paratec, vasp, espresso, siesta, xyz, xsf, and povray.

mat is the native file format of the library. paratec, vasp, espresso,
and siesta represent the formats used by different plane-wave and
local-orbital DFT codes. xyz is a simple format supported by many
molecular viewers, and xsf is the internal format of XCrySDen viewer.
povray stands for a scripting language used by the ray-tracing
program POV-Ray.

The core of the library consists of files common.py, matrix.py, and
matter.py. Script convert.py is a command-line driver that performs
the basic operations supported by the library. Script link.py is a
molecular assembler that can be used to rotate and link two molecules
together. Script gsphere.py generates a real-space grid and a sphere
of G-vectors given lattice parameters and a kinetic energy cutoff.
This helps to estimate the number of unoccupied states needed in GW
calculations. Script average.py takes an average of the scalar field
on the faces or in the volume of the unit cell. This is used to
determine the vacuum level in DFT calculations. Script volume.py
converts the a3Dr file produced by PARATEC or BerkeleyGW to Gaussian
Cube or XCrySDen XSF format.

Each script requires a different set of command-line arguments.
Running individual scripts without arguments displays a list of
all possible command-line arguments and a short description of
each argument.

-----------------------------------------------------------------

Examples:

1. Benzene Charge Density

This example demonstrates how to plot isosurfaces.
Go to directory ./benzene and run ESPRESSO:

$sh link Submit script. Suggested ncpu = 36, walltime = 0:30:00 This will produce the Gaussian Cube file rho.cube containing the charge density of the benzene molecule. For your convenience, the compressed file rho.cube.tgz is included in the ./benzene directory. Let us generate an isosurface that contains 90% of the charge density using the marching cubes algorithm with the smooth triangles and render it in POV-Ray:$ ../surface.x rho_uc.inp
$povray -A0.3 +W640 +H480 +I rho_uc.pov Examine the rho_uc.gif file to find that the pieces of the benzene molecule are placed in the corners of the unit cell. To assemble the pieces together we define a supercell in the rho_sc.inp file. This is done by setting the parameter sc to T and by placing the supercell origin (sco) at position (-0.5 -0.5 -0.5) in crystal coordinates (scu which stands for supercell units is set to latvec). The lattice vectors of the supercell are not changed (scv or supercell vectors in the parameter file). Let us render a new image:$ ../surface.x rho_sc.inp
$povray -A0.3 +W640 +H480 +I rho_sc.pov Now the charge density comes up nice and centered in the middle of the supercell. 2. Nanotube Exciton Wavefunction In this example we will plot an isosurface of the exciton wavefunction. Run ../examples/DFT/swcnt_8-0/ fully. Then go to directory ../examples/DFT/swcnt_8-0/8-absorption/. PlotXct will produce the a3Dr file xct.020_s1.a3Dr containing a wavefunction of the 20th exciton in the (8,0) nanotube. Then volume.py will convert the a3Dr file to Gaussian Cube.$ volume.py ../ESPRESSO/1-scf/in espresso xct.020_s1.a3Dr a3dr xct020.cube cube false abs2 true

The command will produce the Gaussian Cube file xct020.cube that
contains the squared absolute value of the wavefunction
(cplx = abs2) without the sign (phas = false) and the
position of the hole (hole = true). Then surface will generate an
isosurface that contains 90% of the charge density.

$../surface.x xct020.inp You can then render it in POV-Ray (which you must install separately):$ povray -A0.3 +W2560 +H1920 +I xct020.pov

The resulting image xct020.gif is included in the example directory.
Alternately, you can visualize the Cube file directly in XCrySDen.

3. Rock-Salt Lattice

Here you will learn how to make large supercells of bulk crystals.
Go to directory ./rocksalt where you will find the nacl.mat file.
Render it in POV-Ray:

$../convert.py nacl.mat mat nacl.pov povray$ povray -A0.3 +W640 +H480 +I nacl.pov

The unit cell contains only two atoms. Let us make a supercell that
contains a fractional number of unit cells. The supercell is described
by the sc1 file which defines the origin of the supercell, the lattice
vectors of the supercell, and the units in which these quantities
are given. These are equivalent to sco, scv, and scu in the surface
parameter file in the first example. The last line in the sc1 file
corresponds to sct (supercell translation) in the surface parameter
file. We will get back to it later on. Let us render the supercell:

$../convert.py nacl.mat mat nacl_sc1.pov povray supercell sc1$ povray -A0.3 +W640 +H480 +I nacl_sc1.pov

Note the broken bonds on the faces of the supercell.
That is because the supercell contains a fractional number
of the unit cells, so the translational symmetry is broken
which results in the Na-Na and Cl-Cl bonds. We disable the
translational symmetry of the supercell by setting sct to
false (the last line in the sc2 file). This enforces the
translational symmetry of the underlying unit cell structure.
Render the new supercell in POV-Ray:

$../convert.py nacl.mat mat nacl_sc2.pov povray supercell sc2$ povray -A0.3 +W640 +H480 +I nacl_sc2.pov

Now the bonds on the faces of the supercell come out right.

4. Organic Molecule Synthesis

In this example you will assemble the bipolar molecule, bithiophene
naphthalene diimide, from the donor and acceptor units, bithiophene
and naphthalene diimide. Go to directory ./btnd and open files
nd.xyz and bt.xyz in any molecular viewer, for example Jmol.
Identify the atoms you want to link together, these are the two
carbon atoms, # 15 in nd.xyz and # 8 in bt.xyz. You need to remove
the two hydrogen atoms, # 21 in nd.xyz and # 14 in bt.xyz, and place
# 15 and # 8 at the distance of 1.49 Angstrom from each other along
the 15-21-14-8 line. This is done by invoking the following command:

$../link.py nd.xyz xyz bt.xyz xyz btnd.xyz xyz 15 21 8 14 0.0 degree 1.49 angstrom You can also rotate bt.xyz around the 15-21-14-8 axis by an arbitrary angle, although the rotation angle is set to zero in the above command. 5. Estimate the number of unoccupied states for Epsilon and Sigma Go to directory ../examples/DFT/benzene/0-gsphere/ and run the following:$ gsphere.py g_eps.in g_eps.out

Examine input file g_eps.in. It contains the lattice vectors in bohr,
the cutoff energy in Ry (epsilon_cutoff from ../5-gw/epsilon.inp or
screened_coulomb_cutoff from ../5-gw/sigma.inp), '0 0 0' for the FFT
grid to be determined automatically, and 'true' to sort the G-vectors
by their kinetic energies. Examine output file g_eps.out. Look for the
number of G-vectors, ng. You will find 'ng = 2637' meaning that you
will need at least that many unoccupied states. Of course the number
of unoccupied states is a convergence parameter, but gsphere.py gives
you an idea in which range of values should you check the convergence.

Now run the following: