Merge pull request #320 from giovannipizzi/release_3.1

Release 3.1

.gitignore

@@ -3,8 +3,10 @@ postw90.x
 .DS_Store
 make.inc
 w90chk2chk.x
+w90spn2spn.x
 libwannier.a
 libwannier.so
 libwannier.dylib
 *~
-*.x.dSYM
+*.x.dSYM
+.vscode

.pre-commit-config.yaml

@@ -1,3 +1,16 @@
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.2.3
+  hooks:
+  - id: trailing-whitespace
+    files: (?x)^(
+        config/make[.]inc[.\w]*|
+        examples/example\d\d[-]?\w*/.+win
+      )$
+  - id: end-of-file-fixer
+    files: (?x)^(
+        config/make[.]inc[.\w]*|
+        examples/example\d\d[-]?\w*/.+win
+      )$
 - repo: git://github.com/pseewald/fprettify
   sha: v0.3.3
   hooks:
@@ -8,4 +21,3 @@
       )$
     verbose: true
     entry: ./test-suite/tools/fprettify-wrapper.py
-

CHANGELOG.md

@@ -1,12 +1,44 @@
 # CHANGELOG of Wannier90
 
+## v3.1.0 (5th March 2020)
+
+### New features
+
+- Calculation of spin Hall conductivity according to the formalism given in Junfeng Qiao, Jiaqi Zhou, Zhe Yuan and Weisheng Zhao, PRB 98, 214402 (2018) + examples 29 and 30 and tests [[#264]](https://github.com/wannier-developers/wannier90/pull/264)
+
+- Implementation of the SCDM method in Wannier90 for spinor wavefunctions and added example31 for the tutorial [[#277]](https://github.com/wannier-developers/wannier90/pull/277)
+
+- Utility `w90spn2spn.x` for conversion between formatted and unformatted `.spn` files [[#274]](https://github.com/wannier-developers/wannier90/pull/274)
+
+### Various improvements and bugfixes
+
+- Add `install` target for `make`, now `make install` works [[#307]](https://github.com/wannier-developers/wannier90/pull/307)
+
+- Added new documentation and fixed typos [[#308]](https://github.com/wannier-developers/wannier90/pull/308) [[#256]](https://github.com/wannier-developers/wannier90/pull/256) [[#306]](https://github.com/wannier-developers/wannier90/pull/306) [[#300]](https://github.com/wannier-developers/wannier90/pull/300)
+
+- small restructuring of the routines for the AHC calculation with multiple Fermi energies and adaptive refinement [[#289]](https://github.com/wannier-developers/wannier90/pull/289)
+
+- Fix in restart mode (now gathering matrices before dumping `.chk` file) [[#283]](https://github.com/wannier-developers/wannier90/pull/283)
+
+- Fix `pw90common_fourier_R_to_k` subroutines bugs when `use_ws_distance = .true.` [[#273]](https://github.com/wannier-developers/wannier90/pull/273)[[#271]](https://github.com/wannier-developers/wannier90/issues/271)
+
+- Fixes and speed improvements in `pw2wannier90.f90` [[#295]](https://github.com/wannier-developers/wannier90/pull/295) [[#255]](https://github.com/wannier-developers/wannier90/pull/255)
+
+- Bug fixes of `gw2wannier90.py` and `k_mapper.py` [[#294]](https://github.com/wannier-developers/wannier90/pull/294)
+
+- Various bugfixes in input reading and output generation [[#309]](https://github.com/wannier-developers/wannier90/pull/309) [[#290]](https://github.com/wannier-developers/wannier90/pull/290) [[#270]](https://github.com/wannier-developers/wannier90/pull/270) [[#266]](https://github.com/wannier-developers/wannier90/pull/266) [[#258]](https://github.com/wannier-developers/wannier90/pull/258)
+
+- Adding tests for BoltzWann (at least for the electrical conductivity) [[#282]](https://github.com/wannier-developers/wannier90/pull/282)
+
+- Bug fixed in the disentanglement step with SAWFs, especially when running in parallel [[#315]](https://github.com/wannier-developers/wannier90/pull/315)
+
 ## v3.0.0 (27th February 2019)
 
 ### New Wannier90 features
 
 - Selective localization and constrained centres from Marianetti et al. [PRB 90, 165125 (2014)] [[#187]](https://github.com/wannier-developers/wannier90/pull/187) [[#207]](https://github.com/wannier-developers/wannier90/pull/207) [[#206]](https://github.com/wannier-developers/wannier90/pull/206) [[#205]](https://github.com/wannier-developers/wannier90/pull/205)
 
-- Implementation of the SCDM method in Wannier90 [[#167]](https://github.com/wannier-developers/wannier90/pull/167) [[#202]](https://github.com/wannier-developers/wannier90/pull/202) and added an example for the tutorial [[#194]](https://github.com/wannier-developers/wannier90/pull/194). Note that during development we have adapted the interface of the SCDM input flags; Quantum ESPRESSO v6.4 has the current implementation. [[#238]](https://github.com/wannier-developers/wannier90/pull/239)
+- Implementation of the SCDM method in Wannier90 [[#167]](https://github.com/wannier-developers/wannier90/pull/167) [[#202]](https://github.com/wannier-developers/wannier90/pull/202) and added an example for the tutorial [[#194]](https://github.com/wannier-developers/wannier90/pull/194). Note that during development we have adapted the interface of the SCDM input flags; Quantum ESPRESSO v6.4 has the current implementation. [[#238]](https://github.com/wannier-developers/wannier90/pull/238)
 
 
 - Parallelisation of the core Wannier90 routines [[#193]](https://github.com/wannier-developers/wannier90/pull/193) [[#185]](https://github.com/wannier-developers/wannier90/pull/185) [[#173]](https://github.com/wannier-developers/wannier90/pull/173) [[#151]](https://github.com/wannier-developers/wannier90/pull/151) [[#149]](https://github.com/wannier-developers/wannier90/pull/149) [[#125]](https://github.com/wannier-developers/wannier90/pull/125) [[#120]](https://github.com/wannier-developers/wannier90/pull/120) [[#76]](https://github.com/wannier-developers/wannier90/pull/76)
@@ -71,7 +103,9 @@ Moreover, it generates a new file `seedname_band.labelinfo.dat` with information
 
 - Improvements to the Wigner-Seitz detection routines [[#117]](https://github.com/wannier-developers/wannier90/pull/117) [[#109]](https://github.com/wannier-developers/wannier90/pull/109)
 
+- Fix berry_task check for morb, and add check for kpoint_path block in parameters [[#258]](https://github.com/wannier-developers/wannier90/pull/258)
 
+- Use 64 bit integer in io_wallclocktime [[#266]](https://github.com/wannier-developers/wannier90/pull/266)
 
 
 

Makefile

@@ -8,7 +8,19 @@ TAR := $(shell if which gnutar 1>/dev/null 2> /dev/null; then echo gnutar; else
 
 default: wannier post
 
-all: wannier lib post w90chk2chk w90pov w90vdw
+PREFIX ?= /usr
+
+install: default
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	for x in wannier90.x postw90.x w90chk2chk.x w90spn2spn.x ; do \
+		if [ -f "$$x" ]; then install -m755 "$$x" "$(DESTDIR)$(PREFIX)/bin/$$x"; fi; \
+	done
+	if [ -f "utility/w90pov/w90pov" ]; then install -m755 "utility/w90pov/w90pov" "$(DESTDIR)$(PREFIX)/bin/w90pov"; fi;
+	if [ -f "utility/w90vdw/w90vdw.x" ]; then install -m755 "utility/w90vdw/w90vdw.x" "$(DESTDIR)$(PREFIX)/bin/w90vdw.x"; fi;
+	install -d $(DESTDIR)$(PREFIX)/lib/
+	if [ -f "libwannier.a" ]; then install -m644 "libwannier.a" "$(DESTDIR)$(PREFIX)/lib/libwannier.a"; fi;
+
+all: wannier lib post w90chk2chk w90pov w90vdw w90spn2spn
 
 doc: thedoc
 
@@ -18,6 +30,9 @@ serialobjs: objdir
 w90chk2chk: objdir serialobjs
 	(cd $(ROOTDIR)/src/obj && $(MAKE) -f $(REALMAKEFILE) w90chk2chk)
 
+w90spn2spn: objdir serialobjs
+	(cd $(ROOTDIR)/src/obj && $(MAKE) -f $(REALMAKEFILE) w90spn2spn)
+
 wannier: objdir serialobjs
 	(cd $(ROOTDIR)/src/obj && $(MAKE) -f $(REALMAKEFILE) wannier)
 
@@ -58,7 +73,7 @@ clean:
 	cd $(ROOTDIR)/test-suite && ./clean_tests
 
 veryclean: clean
-	cd $(ROOTDIR) && rm -f wannier90.x postw90.x libwannier.a w90chk2chk.x
+	cd $(ROOTDIR) && rm -f wannier90.x postw90.x libwannier.a w90chk2chk.x w90spn2spn.x
 	cd $(ROOTDIR)/doc && rm -f user_guide.pdf tutorial.pdf
 	cd $(ROOTDIR)/doc/user_guide && rm -f user_guide.ps
 	cd $(ROOTDIR)/doc/tutorial && rm -f tutorial.ps 
@@ -68,14 +83,14 @@ thedoc:
 	$(MAKE) -C $(ROOTDIR)/doc/user_guide 
 	$(MAKE) -C $(ROOTDIR)/doc/tutorial 
 
-# For now hardcoded to 3.0.0, and using HEAD
+# For now hardcoded to 3.1.0, and using HEAD
 # Better to get the version from the io.F90 file and use
-# the tag (e.g. v3.0.0) instead of HEAD
+# the tag (e.g. v3.1.0) instead of HEAD
 dist: 
-	cd $(ROOTDIR) && git archive HEAD --prefix=wannier90-3.0.0/ -o wannier90-3.0.0.tar.gz
+	cd $(ROOTDIR) && git archive HEAD --prefix=wannier90-3.1.0/ -o wannier90-3.1.0.tar.gz
 
 dist-legacy:
-	@(cd $(ROOTDIR) && $(TAR) -cz --transform='s,^\./,wannier90-3.0/,' -f wannier90-3.0.tar.gz \
+	@(cd $(ROOTDIR) && $(TAR) -cz --transform='s,^\./,wannier90-3.1/,' -f wannier90-3.1.tar.gz \
 		./src/*.?90 \
 		./src/postw90/*.?90 \
 		./autodoc/README.txt \
@@ -202,4 +217,4 @@ objdirp:
 		then mkdir src/objp ; \
 	fi ) ;
 
-.PHONY: wannier default all doc lib libs post clean veryclean thedoc dist test-serial test-parallel dist-lite objdir objdirp serialobjs tests
+.PHONY: wannier default all doc lib libs post clean veryclean thedoc dist test-serial test-parallel dist-lite objdir objdirp serialobjs tests w90spn2spn install

README.install

@@ -48,6 +48,7 @@
                    the user guide)
    make w90vdw     build the van der Waals code
    make w90pov     build the ray-tracing code
+   make install    install the built binaries
    make tests      run test cases
    make doc        build the documentation
    make dist       make a tar-ball of the distribution
@@ -58,6 +59,11 @@
  'make -j NN' will allow compilation using NN multiple threads.
  On a multicore CPU this will build the executables in a shorter time.
 
+ 'make install' supports DESTDIR and PREFIX variables.
+ Executables will be installed into $(DESTDIR)$(PREFIX)/bin directory,
+ libraries will be installed into $(DESTDIR)$(PREFIX)/lib directory.
+ The default DESTDIR is empty, and the default PREFIX is /usr.
+
  In order to compile the postw90.x executable in its parallel version, you have
  to specify 
   COMMS=mpi
@@ -78,7 +84,7 @@
   LAPACK can be obtained from the netlib website. It also includes a 
   non-optimised BLAS.
      http://www.netlib.org/lapack/
-     
+
 
 Linux x86,x86-64
 ----------------

README.rst

@@ -28,13 +28,25 @@ How to cite
 +++++++++++
 Please cite the following paper in any publications arising from the use of 
 this code:
+
+  G. Pizzi, V. Vitale, R. Arita, S. Blügel, F. Freimuth, G. Géranton, M. Gibertini, 
+  D. Gresch, C. Johnson, T. Koretsune, J Ibañez-Azpiroz, H. Lee, J.M. Lihm, 
+  D. Marchand, A. Marrazzo, Y. Mokrousov, J.I. Mustafa, Y. Nohara, Y. Nomura, 
+  L. Paulatto, S. Poncé, T. Ponweiser, J. Qiao, F. Thöle, S.S. Tsirkin, 
+  M. Wierzbowska, N. Marzari, D. Vanderbilt, I. Souza, A.A. Mostofi, J.R. Yates, 
+  Wannier90 as a community code: new features and applications, 
+  `J. Phys. Cond. Matt. 32, 165902`_ (2020)
+
+.. _J. Phys. Cond. Matt. 32, 165902: https://doi.org/10.1088/1361-648X/ab51ff
+
+If you are using versions 2.x of the code, cite instead:
 
   A.A. Mostofi, J.R. Yates, G. Pizzi, Y.S. Lee, I. Souza, 
   D Vanderbilt, N Marzari, *An updated version of wannier90: A tool for 
   obtaining maximally-localised Wannier functions*, 
   `Comput. Phys. Commun. 185, 2309 (2014)`_ 
 
-.. _Comput. Phys. Commun. 185, 2309 (2014): http://dx.doi.org/10.1016/j.cpc.2014.05.003
+.. _Comput. Phys. Commun. 185, 2309 (2014): http://doi.org/10.1016/j.cpc.2014.05.003
 
 For the method please cite:
 
@@ -95,6 +107,7 @@ In addition to the Wannier90 Developer Group, the other authors of Wannier90 v.3
 * Takashi Koretsune (Tohoku University and JST PRESTO, JP): Symmetry-adapted Wannier functions, non-collinear spin with ultrasoft in pw2wannier90
 * Julen Ibañez-Azpiroz (Universidad del Pais Vasco, ES): shift-current calculation
 * Hyungjun Lee (EPFL, CH): Spinor-valued WFs, parallelisation of the core Wannier90 routines
+* Jae-Mo Lihm (Seoul National University, KR): SCDM-k implementation for non-collinear spin in pw2wannier90
 * Daniel Marchand (EPFL, CH): AiiDA-Wannier90 interface
 * Antimo Marrazzo (EPFL, CH): GW bands interpolation, AiiDA-Wannier90 interface
 * Yuriy Mokrousov (FZ  Jülich, DE): Parallelization of the core routines
@@ -157,7 +170,7 @@ Wannier90 Version 1.0 was written by:
 * Jonathan R. Yates  (University of Oxford, GB)
 * Young-Su Lee       (KIST, KR)
 
-Wannier90 is based on Fortran 77 codes written by:
+Wannier90 is based on the [Wannier Fortran 77 code](http://www.wannier.org/history/) by:
 
 * Nicola Marzari (EPFL, CH)
 * Ivo Souza (Universidad del Pais Vasco, ES)

config/make.inc.alpha

@@ -3,7 +3,6 @@
 #======
 
 F90    = f90
-FCOPTS = -fast  
-LDOPTS = -fast 
+FCOPTS = -fast
+LDOPTS = -fast
 LIBS   = -lcxml
-

config/make.inc.g95

@@ -2,7 +2,7 @@
 # g95
 #===================
 F90 = g95
-FCOPTS = -O2 
+FCOPTS = -O2
 LDOPTS = -O2
 
 
@@ -18,6 +18,3 @@ LDOPTS = -O2
 #=======================
 #LIBDIR = /usr/local/lib
 #LIBS = -L$(LIBDIR)  -llapack -lblas
-
-
-

config/make.inc.gfort

@@ -4,14 +4,14 @@
 F90 = gfortran
 
 #Add next two lines for parallel postw90. Choose the correct name of the mpi f90 wrapper
-#COMMS  = mpi 
+#COMMS  = mpi
 #MPIF90 = mpgfortran #mpif90
 
-FCOPTS = -O3 
+FCOPTS = -O3
 LDOPTS =
 
 #Next two lines are good for debugging
-#FCOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
+#FCOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
 #LDOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
 
 
@@ -25,7 +25,7 @@ LDOPTS =
 #=======================
 # NETLIB LAPACK and BLAS
 #=======================
-#LIBDIR = /rscratch/jry20/LIB/gfortran 
+#LIBDIR = /rscratch/jry20/LIB/gfortran
 #LIBS = -L$(LIBDIR)  -llapack -lblas
 
 #=======================
@@ -35,8 +35,3 @@ LDOPTS =
 # on Ubuntu
 #=======================
 LIBS = -llapack -lblas
-
-
-
-
-

config/make.inc.gfort.dynlib

@@ -4,14 +4,14 @@
 F90 = gfortran
 
 #Add next two lines for parallel postw90. Choose the correct name of the mpi f90 wrapper
-#COMMS  = mpi 
+#COMMS  = mpi
 #MPIF90 = mpgfortran #mpif90
 
 FCOPTS = -O3 -fPIC
 LDOPTS = -fPIC
 
 #Next two lines are good for debugging
-#FCOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
+#FCOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
 #LDOPTS = -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
 
 
@@ -25,7 +25,7 @@ LDOPTS = -fPIC
 #=======================
 # NETLIB LAPACK and BLAS
 #=======================
-#LIBDIR = /rscratch/jry20/LIB/gfortran 
+#LIBDIR = /rscratch/jry20/LIB/gfortran
 #LIBS = -L$(LIBDIR)  -llapack -lblas
 
 #=======================
@@ -35,8 +35,3 @@ LDOPTS = -fPIC
 # on Ubuntu
 #=======================
 LIBS = -llapack -lblas
-
-
-
-
-

config/make.inc.gfort.travisci

@@ -4,12 +4,12 @@
 F90 = gfortran
 
 # Keep these committed - we test for the time being only the serial version
-#COMMS  = mpi 
+#COMMS  = mpi
 #MPIF90 = mpgfortran #mpif90
 
 # Options for debugging  When we move to 4.9 add -fsanitize=leak
-FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
-LDOPTS =  -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
+FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
+LDOPTS =  -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace
 
 #=======================
 # System LAPACK and BLAS
@@ -18,4 +18,3 @@ LDOPTS =  -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-poin
 # on Ubuntu
 #=======================
 LIBS = -llapack -lblas
-

config/make.inc.ifort

@@ -5,8 +5,8 @@
 F90 = ifort
 COMMS=mpi
 MPIF90=mpiifort
-FCOPTS=-O2 
-LDOPTS=-O2 
+FCOPTS=-O2
+LDOPTS=-O2
 
 #========================================================
 # Intel mkl libraries. Set LIBPATH if not in default path
@@ -20,4 +20,3 @@ LIBS   =  -L$(LIBDIR) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lpthread
 #=======================
 #LIBDIR = /usr/local/lib
 #LIBS = -L$(LIBDIR)  -llapack -lf77blas -lcblas -latlas
-

config/make.inc.ifort_tcm

@@ -7,7 +7,7 @@ F90 = ifort
 COMMS=mpi
 MPIF90=mpifort
 FCOPTS = -O3
-LDOPTS = 
+LDOPTS =
 
 #useful debuf options
 #FCOPTS=-Ddebug -O0 -g -fno-omit-frame-pointer -debug extended -traceback -C -Ddebug -stand f95 -warn all
@@ -17,11 +17,10 @@ LDOPTS =
 # Intel mkl libraries. Set LIBPATH if not in default path
 #========================================================
 
-LIBS   =  -L$(LIBDIR)   -Bstatic -lmkl 
+LIBS   =  -L$(LIBDIR)   -Bstatic -lmkl
 
 #=======================
 # ATLAS Blas and LAPACK
 #=======================
 #LIBDIR = /usr/local/lib
 #LIBS = -L$(LIBDIR)  -llapack -lf77blas -lcblas -latlas
-