Merge branch 'release/v.1.1.0'

ChangeLog.md

@@ -1,3 +1,36 @@
+# Ver. 1.1.0 (2019-5-1)
+
+## New
+
+- An interface to OpenMX code (contributed by Yuto Tanaka)
+- Compressive sensing approach (``LMODEL = enet``) in alm code. Many new variables related to the compressive sensing are also added. See the document page for details.
+- ``SPARSE`` and ``SPARSESOLVER`` tags in alm code
+- ``DOS``-tag in anphon code
+- A python script scph_to_qe.py that converts the result of a SCPH calculation to Quantum ESPRESSO force-constant format.
+
+## Changes
+
+- Default value of ``ICONST`` is changed to ``ICONST = 11``
+- Python scripts now work with python3 as well as python2
+- Python interface scripts are move to tools/interface
+- Default values for ``MASS``- and ``ISOFACT``-tags are implemented
+- Implement a sparse version of rref, which improves the performance of alm significantly.
+- Performance improvements of anphon code.
+- ``DFILE`` and ``FFILE`` in alm code are now deprecated. Use ``DFSET`` instead.
+- ``&fitting`` field in alm is replaced with ``&optimize`` field.
+
+## Fix
+
+- Fix a minor bug in calc_damping_tetrahedron. The phonon linewidths at high temperatures and the thermal conductivityies were not affected by this minor error. In very low temperature region (< 10 K), the thermal conductivity may have been underestimated.
+- Fix other minor bugs
+
+# Ver. 1.0.1 (2017-11-21)
+
+## Fix
+- Fixed a minor issue in the previous version
+
+
+
 # Ver. 1.0.2 (2018-1-29)
 
 ## New

README.md

@@ -3,7 +3,7 @@
 [![License][license-image]][license-url]
 [![Doc status][docs-image]][docs-url]
 
-### Version 1.0.2
+### Version 1.1.0
 ![alt ALAMODE](./docs/img/alamode.png)
 
 
@@ -13,7 +13,7 @@
 
 ALAMODE is a scientific software designed for analyzing lattice anharmonicity
 and  lattice thermal conductivity of solids. By using an external DFT package
-such as  VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic
+such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic
 force constants  straightforwardly with ALAMODE. Using the calculated anharmonic
 force constants, you can also estimate lattice thermal conductivity, phonon
 linewidth, and other anharmonic phonon properties from first principles.
@@ -25,7 +25,7 @@ linewidth, and other anharmonic phonon properties from first principles.
 * Extraction of harmonic and anharmonic force constants based on the supercell approach
 * Applicable to any crystal structures and low-dimensional systems
 * Accurate treatment of translational and rotational invariance
-* Interface to VASP, Quantum-ESPRESSO, xTAPP, and LAMMPS codes
+* Interface to VASP, Quantum-ESPRESSO, OpenMX, xTAPP, and LAMMPS codes
 * Parallelization with MPI+OpenMP
 
 ### Harmonic properties
@@ -57,6 +57,7 @@ linewidth, and other anharmonic phonon properties from first principles.
 * Boost C++ library
 * FFT library
 * Eigen3 library
+* spglib
 
 ## Download
 
@@ -75,7 +76,7 @@ If you download the github version, please use the 'master' branch.
 The directories alm/, anphon/, and tools/ contain separate Makefiles.
 Please modify the Makefiles appropriately by changing variables such as 
 CXX, CXXFLAGS, or MPICXX. Then, execute "make" will create the binary for
-each program.
+each program. Please see the documentation for more details.
 
 
 ## Documentation
@@ -86,7 +87,7 @@ http://alamode.readthedocs.io
 
 
 ## License
-Copyright (c) 2014--2017 Terumasa Tadano
+Copyright (c) 2014--2019 Terumasa Tadano
 This software is released under the MIT license. 
 For license rights and limitations, see LICENSE.txt file.
 
@@ -97,7 +98,7 @@ Terumasa Tadano (National Institute for Materials Science, Japan)
 
 * Tatsuro Nishimoto (Univ. Tokyo)
 * Yusuke Oba (Univ. Tokyo)
-
+* Atsushi Togo (Kyoto Univ.)
 
 
 [license-image]: https://img.shields.io/github/license/ttadano/alamode.svg

alamode.sln

@@ -1,7 +1,7 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio 14
-VisualStudioVersion = 14.0.25123.0
+# Visual Studio Version 16
+VisualStudioVersion = 16.0.28803.202
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "alm", "alm\alm.vcxproj", "{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}"
 EndProject
@@ -22,13 +22,15 @@ Global
 		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Debug|x64.ActiveCfg = Debug|Win32
 		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Release|Win32.ActiveCfg = Release|Win32
 		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Release|Win32.Build.0 = Release|Win32
-		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Release|x64.ActiveCfg = Release|Win32
+		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Release|x64.ActiveCfg = Release|x64
+		{0FFEA662-D4F1-4D18-A920-B61EE02A7F21}.Release|x64.Build.0 = Release|x64
 		{80B34241-B404-47A5-B4C6-DA735D121433}.Debug|Win32.ActiveCfg = Debug|Win32
 		{80B34241-B404-47A5-B4C6-DA735D121433}.Debug|Win32.Build.0 = Debug|Win32
 		{80B34241-B404-47A5-B4C6-DA735D121433}.Debug|x64.ActiveCfg = Debug|Win32
 		{80B34241-B404-47A5-B4C6-DA735D121433}.Release|Win32.ActiveCfg = Release|Win32
 		{80B34241-B404-47A5-B4C6-DA735D121433}.Release|Win32.Build.0 = Release|Win32
-		{80B34241-B404-47A5-B4C6-DA735D121433}.Release|x64.ActiveCfg = Release|Win32
+		{80B34241-B404-47A5-B4C6-DA735D121433}.Release|x64.ActiveCfg = Release|x64
+		{80B34241-B404-47A5-B4C6-DA735D121433}.Release|x64.Build.0 = Release|x64
 		{93B2B654-5EEE-46E4-8DCF-8E6051B6C1ED}.Debug|Win32.ActiveCfg = Debug|Win32
 		{93B2B654-5EEE-46E4-8DCF-8E6051B6C1ED}.Debug|Win32.Build.0 = Debug|Win32
 		{93B2B654-5EEE-46E4-8DCF-8E6051B6C1ED}.Debug|x64.ActiveCfg = Debug|x64
@@ -41,4 +43,7 @@ Global
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {0545154B-4355-4AA5-AC7F-B4206208E703}
+	EndGlobalSection
 EndGlobal

alm/Makefile.linux

@@ -6,11 +6,11 @@
 #-----------------------------------------------
 
 CXX = icpc 
-CXXFLAGS = -O2 -xHOST -openmp -std=c++11
-INCLUDE = -I../include
+CXXFLAGS = -O2 -xHOST -qopenmp -std=c++11
+INCLUDE = -I../include -I$(HOME)/include -I$(SPGLIB_ROOT)/include
 
 CXXL = ${CXX}
-LDFLAGS = -mkl
+LDFLAGS = -mkl -L$(SPGLIB_ROOT)/lib -lsymspg
 
 LAPACK = 
 LIBS = ${LAPACK}
@@ -24,9 +24,7 @@ LIBS = ${LAPACK}
 
 PROG = alm
 
-CXXSRC= alamode.cpp constraint.cpp error.cpp fcs.cpp files.cpp \
-	fitting.cpp input.cpp interaction.cpp main.cpp memory.cpp \
-	patterndisp.cpp symmetry.cpp system.cpp timer.cpp writes.cpp 
+CXXSRC= $(wildcard *.cpp)
 
 OBJS= ${CXXSRC:.cpp=.o}
 

alm/Makefile.osx

@@ -9,12 +9,12 @@
 # OpenMP-enabled gcc can be installed via homebrew
 CXX = g++-8
 CXXFLAGS = -O2 -fopenmp -std=c++11
-INCLUDE = -I../include
+INCLUDE = -I../include -I$(HOME)/include -I$(SPGLIB_ROOT)/include
 
 CXXL = ${CXX}
-LDFLAGS = -lgomp
+LDFLAGS = -lgomp -L$(SPGLIB_ROOT)/lib -lsymspg
 
-LAPACK = -llapack
+LAPACK = -llapack -lblas
 LIBS = ${LAPACK}
 
 #-----------------------------------------------
@@ -26,9 +26,7 @@ LIBS = ${LAPACK}
 
 PROG = alm
 
-CXXSRC= alamode.cpp constraint.cpp error.cpp fcs.cpp files.cpp \
-	fitting.cpp input.cpp interaction.cpp main.cpp memory.cpp \
-	patterndisp.cpp symmetry.cpp system.cpp timer.cpp writes.cpp 
+CXXSRC= $(wildcard *.cpp)
 
 OBJS= ${CXXSRC:.cpp=.o}
 

alm/Makefile.osx_clang

@@ -0,0 +1,50 @@
+.SUFFIXES: .h .cpp
+#-----------------------------------------------
+# Makefile for the program 'ALM'.
+# Please modify the variables properly.
+# We recommend to use Intel c++ compiler.
+#-----------------------------------------------
+
+# Use clang++ to use hdf5 installed via homebrew
+CXX = g++
+CXXFLAGS = -O2 -std=c++11
+INCLUDE = -I../include -I$(HOME)/include -I$(SPGLIB_ROOT)/include
+
+CXXL = ${CXX}
+LDFLAGS = -L$(SPGLIB_ROOT)/lib -lsymspg
+#LDFLAGS = -L/usr/local/lib -lhdf5_cpp -lhdf5 -lsymspg
+
+LAPACK = -llapack -lblas
+LIBS = ${LAPACK}
+
+#-----------------------------------------------
+# General rules 
+#-----------------------------------------------
+
+.cpp.o:
+	${CXX} ${CXXFLAGS} ${INCLUDE} -c $<
+
+PROG = alm
+
+CXXSRC= alm.cpp alm_cui.cpp input_parser.cpp input_setter.cpp constraint.cpp fcs.cpp files.cpp \
+	optimize.cpp cluster.cpp main.cpp rref.cpp \
+	patterndisp.cpp symmetry.cpp system.cpp timer.cpp writer.cpp 
+
+OBJS= ${CXXSRC:.cpp=.o}
+
+default: alm
+
+all: ${PROG}
+
+alm: ${OBJS}
+	${CXXL} ${LDFLAGS} -o $@ ${OBJS} ${LIBS}
+
+clean:
+	rm -f ${OBJS}
+
+.PHONY: clean
+
+depend:
+	gcc -MM *.cpp > .depend
+
+-include .depend