Description:
Density functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases.
We can find lots of tutorials, but this is a good one!
There some programs to do the task. A very good one is Quantum Espresso, which is free under GPL licence.
Here some hint of how to configure it.
Quantum espresso configuration
is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
(tested with 6.0.0 version)
http://www.hpcadvisorycouncil.com/pdf/ESPRESSO_Best_Practices.pdf
https://glennklockwood.blogspot.com/2014/02/quantum-espresso-compiling-and-choice.html
Some usefull links:
-> Link advisor to configure FFTW environment variables to run with intel’s mkl
-> Usefull discussions (1), (2)
-> Explicit offload for Quantum ESPRESSO
-> Installing Quantum Espresso with Intel Parallel Studio and OpenMPI
-> Quantum ESPRESSO* for Intel® Xeon Phi™ Coprocessor
-> Intel® Parallel Studio XE 2017
-> Using the ifortvars File to Specify Location of Components
-> Intel® Fortran Compiler 16.0 User and Reference Guide
________________________________________________________________
First things first!
Follow this up in order to compile QE using Intel’s compilers, mkl and mpi.
After installing Intel’s Parallel Studio, source compiler, mkl and mpi variables.
It could be included to the bashrc file:
#compilers source
source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64
source /opt/intel/compilers_and_libraries/linux/mkl/bin/mklvars.sh intel64
source /opt/intel/compilers_and_libraries/linux/mpi/bin64/mpivars.sh
the paths point out to the installation folders.
compilervar.sh and mklvar.sh are sourced using <arch> intel64
This should give to QE’s configure the correct paths.
Configure QE explicitly indicating the intel’s compilers,
$ export FC=mpiifort
$ export F90=ifort
$ export F77=ifort
$ export MPIF90=mpiifort
$ export CC=mpicc
$ ./configure –enable-openmp –enable-parallel -with-scalapack=intel
or
$ ./configure –enable-parallel -with-scalapack=intel F90=ifort F77=ifort MPIF90=mpiifort CC=mpicc LIBDIRS=”/opt/intel/compilers_and_libraries/linux/mkl/lib/intel64″
It should produce a make.inc file like this (comments were removed)
======================================
.SUFFIXES :
.SUFFIXES : .o .c .f .f90
.f90.o:
$(MPIF90) $(F90FLAGS) -c $<
# .f.o and .c.o: do not modify
.f.o:
$(F77) $(FFLAGS) -c $<
.c.o:
$(CC) $(CFLAGS) -c $<
MANUAL_DFLAGS =
DFLAGS = -D__INTEL -D__DFTI -D__MPI
FDFLAGS = $(DFLAGS) $(MANUAL_DFLAGS)
IFLAGS = -I$(TOPDIR)/include -I../include/ -I/opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/include
MOD_FLAG = -I
MPIF90 = mpiifort
#F90 = ifort
CC = icc
F77 = ifort
CPP = cpp
CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS)
CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O2 -assume byterecl -g -traceback
FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback
FFLAGS_NOMAIN = -nofor_main
LD = mpiifort
LDFLAGS = -static-intel
LD_LIBS =
BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
BLAS_LIBS_SWITCH = external
LAPACK_LIBS = -mkl=parallel
LAPACK_LIBS_SWITCH = external
SCALAPACK_LIBS =
FFT_LIBS =
HDF5_LIB =
MPI_LIBS =
MASS_LIBS =
AR = ar
ARFLAGS = ruv
RANLIB = ranlib
FLIB_TARGETS = all
LIBOBJS = $(TOPDIR)/clib/clib.a $(TOPDIR)/iotk/src/libiotk.a
LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) ${HDF5_LIB} $(LD_LIBS)
WGET = wget -O
PREFIX = /usr/local
================================
Note that FFT_LIBS path it was not recognized and should generate a crash during the make process. Using the Intel’s Link advisor we could get the correct links between mkl and FFT. It should produce something like (https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/)
-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl
So, replace
FFT_LIBS =
with
FFT_LIBS = -L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl
If configure proceed without errors, make all executables (or the ones needed). Type
$ make all
Testing installation
Inside the software folders it is possible to find examples. For example,
$<qe_install_folder>/pw/examples
run all examples using the given script
$ ./run_all_examples
For newer versions of QE (>6, for instance) there is a test-suite script. Search for the folder /test-suite and type make. It should return the available options for making. Yelds something like
===================
To run Quantum ESPRESSO test-suite, type at the shell prompt:
make target
where <target> identifies an action
run-tests : run-tests-serial (default)
run-tests-serial : run all tests in SERIAL
run-tests-parallel : run all tests in PARALLEL (4 MPI)
compare : compare last output generated with reference
clean : clean output (our/err files) of all tests
For additional advanced commands and settings please manually inspect
ENVIRONMENT and Makefile files
=====================
Use, for example,
$make run-tests-parallel (takes a fairly long time to proceed)
Linking to QE executables
All executable files are withing the <intallation_folder>/bin. Export the path to the bashrc file allow for executing from a non-specific folder
export PATH=$PATH:/<installation_folder>/bin
Graphical User Interface – PWGUI
Within the QE it could be found the GUI folder. Inside of it there are some option for the GUI. For pw-like files PWGUI is a good one.
From README we have
The main purpose of the PWgui is to facilitate the creation and manipulation (editing) of input files for PWscf set of programs. It is possible to run the PWscf programs by using the GUI. This feature
requires to set the path of the PWscf executables via “File–>Settings” menu (tab: PWscf settings). The GUI can also use the XCRYSDEN program (http://www.xcrysden.org/) for the visualization of
atomic structures from the pw.x input/output files, or for the visualization of properties calculated via the sequence: pw.x–>pp.x (when the property was saved into an XSF file).
Currently, the following PWscf programs (modules) are supported:
* pw.x
* neb.x’s neb.dat
* ph.x
* pp.x
* projwfc.x
* bands.x
* dos.x
* d3.x
* ld1.x (atomic)
In order to use it, inside PWGUI folder, run the script pwgui. Type
$ ./pwgui
The path could also be exported and sourced to the bashrc file
export PATH=$PATH:/<intallation_folder>/GUI/PWgui
DONE!!!!