Tutorial on installing Alamode on a Linux machine

Xijun Wang

02/19/2021

Introduction

ALAMODE is an open source 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 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.

Official site: https://alamode.readthedocs.io/en/latest/

Key Features of Alamode

General

• 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

• Mainly written in C++, parallelized with MPI+OpenMP

Harmonic properties

• Phonon dispersion

• Phonon DOS, atom-projected phonon DOS

• Two-phonon DOS

• Vibrational thermodynamic functions (heat capacity, entropy, free energy)

• Mean-square displacement

• Animation and visualization of phonon modes (requires VMD or XCrysDen)

• 3-phonon scattering phase space

• Phonon-isotope scattering rate

• Participation ratio for analyzing the localization of phonon modes

Anharmonic properties

• Grüneisen parameter via cubic force constants

• Lattice thermal conductivity by BTE-RTA

• Cumulative thermal conductivity

• Phonon linewidth due to 3-phonon interactions

• Phonon frequency shift due to 3- and 4-phonon interactions

• Temperature-dependent effective potential method

• Self-consistent phonon (SCPH) calculation

• Anharmonic vibrational free-energy

Preparations Before Installation

Load basic modules (MPI Compier, MKL library):

[xwang99@login02 tools]$ module list

Currently Loaded Modulefiles:

1) conda 2) intel/2016.0.109 3) intel_mpi/2016 4) mkl/2017

Install or link required libraries (if necessary):

1. boost: https://www.boost.org/users/history/version_1_64_0.html

tar xvf boost_1_64_0.tar.bz2

mkdir include

cd /your directory A/include

ln -s /your directory A/boost_1_64_0/boost .

cd ..

2. eigen: https://gitlab.com/libeigen/eigen/-/archive/3.3.3/eigen-3.3.3.tar.bz2

tar xvf eigen-3.3.3.tar.bz2

cd /your directory A/include

ln -s /your directory A/eigen-3.3.3/Eigen .

cd ..

3. cmake:https://cmake.org/download/

tar xvf cmake-3.20.0-rc1-linux-x86_64.tar.gz

set PATH = (/your directory A/cmake-3.20.0-rc1-linux-x86_64/bin:$PATH) # For csh users

#export PATH=/your directory A/cmake-3.20.0-rc1-linux-x86_64/bin:$PATH # For bash users

4. spglib: https://github.com/spglib/spglib/tags

tar zxvf spglib-1.16.0.tar.gz

cd spglib-1.16.0

mkdir build

cd build

cmake -DCMAKE_INSTALL_PREFIX="" .. # Or /your directory A/cmake-3.20.0-rc1-linux-x86_64/bin/cmake -DCMAKE_INSTALL_PREFIX="" ..

make

make DESTDIR=/your directory A/software install

set SPGLIB_ROOT=/your directory A/software # For csh users

#export SPGLIB_ROOT=/your directory A/software # For bash users

Alamode installation

Download the package from https://sourceforge.net/projects/alamode/

There are three software in the package (alm, anphon, tools), let's compile them one by one.

1. Compile alm

tar xvf alamode-1.1.0.tar.gz

cd /your directory A/alamode-1.1.0

# Compile alm

cd /your directory A/alamode-1.1.0/alm

cp Makefile.linux Makefile

[xwang99@login02 alm]$ cat Makefile

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

.SUFFIXES: .h .cpp

#-----------------------------------------------

# Makefile for the program 'ALM'.

# Please modify the variables properly.

# We recommend to use Intel c++ compiler.

#-----------------------------------------------

CXX = icpc # Select suitable compiler, here we just use icpc

CXXFLAGS = -O2 -xHOST -qopenmp -std=c++11

INCLUDE = -I../include -I$(SPGLIB_ROOT)/include # May also use absolute path, such as -I//your directory A/include -I/your directory A/spglib-1.16.0/software/include

CXXL = ${CXX}

LDFLAGS = -mkl -L$(SPGLIB_ROOT)/lib64 -lsymspg # May also use absolute path, LDFLAGS = -mkl -L/your directory A/spglib-1.16.0/software/lib64 -lsymspg

LAPACK =

LIBS = ${LAPACK}

#-----------------------------------------------

# General rules

#-----------------------------------------------

.cpp.o:

${CXX} ${CXXFLAGS} ${INCLUDE} -c $<

PROG = alm

CXXSRC= $(wildcard *.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

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

make -j

[xwang99@login02 alm]$ ls alm

alm

2. Compile anphon

# Compile anphon

cd /your directory A/alamode-1.1.0/anphon

cp Makefile.linux Makefile

[xwang99@login02 alm]$ cat Makefile

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

.SUFFIXES: .h .cpp

#-----------------------------------------------

# Makefile for the program 'ANPHON'.

# Please modify the variables properly.

# We recommend to use Intel c++ compiler.

#-----------------------------------------------

MPICXX = mpicxx #Select suitable compiler

CXXFLAGS = -O3 -xHOST -openmp -std=c++11

INCLUDE = -I../include -I/your directory A/include

LINKER = ${MPICXX}

LDFLAGS = -mkl

LAPACK =

LIBS = ${LAPACK}

#----------------------------------------------

# General rules

#----------------------------------------------

.cpp.o:

${MPICXX} ${CXXFLAGS} ${INCLUDE} -c $<

PROG = anphon

CXXSRC = $(wildcard *.cpp)

OBJS= ${CXXSRC:.cpp=.o}

default: anphon

all: ${PROG}

anphon: ${OBJS}

${LINKER} ${LDFLAGS} -o $@ ${OBJS} ${LIBS}

clean:

rm -f ${OBJS}

.PHONY: clean

depend:

gcc -MM *.cpp > .depend

-include .depend

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

make -j

[xwang99@login02 alm]$ ls alm

anphon

3. Compile tools

# Compile tools

cd /your directory A/alamode-1.1.0/tools

[xwang99@login02 alm]$ cat Makefile

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

.SUFFIXES: .h .cpp

#-----------------------------------------------

# Makefile for 'tools' directory

# Please modify the variables properly.

# We recommend to use Intel c++ compiler.

#-----------------------------------------------

#Intel compiler

#CXX = icpc

# OSX (gcc)

CXX = icpc

# OSX (clang)

#CXX = g++

CXXFLAGS = -O2 -std=c++11

# Add the directory containing boost header files here

INCLUDE = -I../include -I/your directory/include

#----------------------------------------------

# General rules

#----------------------------------------------

.cpp.o:

${CXX} ${CXXFLAGS} ${INCLUDE} -c $<

PROG = analyze_phonons qe2alm dfc2

CXXSRC = analyze_phonons.cpp qe2alm.cpp dfc2.cpp

OBJS= ${CXXSRC:.cpp=.o}

default: all

all: ${PROG}

analyze_phonons: analyze_phonons.o

${CXX} ${CXXFLAGS} -o $@ $<

qe2alm: qe2alm.o

${CXX} ${CXXFLAGS} -o $@ $<

dfc2: dfc2.o

${CXX} ${CXXFLAGS} -o $@ $<

clean:

rm -f ${OBJS}

.PHONY: clean

depend:

gcc -MM *.cpp > .depend

-include .depend

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

make -j

[xwang99@login02 alm]$ ls analyze_phonons qe2alm dfc2

analyze_phonons qe2alm dfc2

The last step is to dynamically link the required library to the alm:

setenv LD_LIBRARY_PATH /your directory A/spglib-1.16.0/software/lib64:$LD_LIBRARY_PATH # For csh

#export LD_LIBRARY_PATH=/your directory A/spglib-1.16.0/software/lib64:$LD_LIBRARY_PATH # For bash

#May need to add this command to ~/.bashrc

Notes

Make sure all the key compilers and libraries are correctly installed, and linked.

Make sure that all paths in the Makefiles are set correctly.

If fftw library is required during the process of compilation, the $(MKLROOT) path should be added to the Makefile:

INCLUDE = -I../include -I/your directory A/include -I$(MKLROOT)/include/fftw