From d476a9bb392acbfc0af953d5f1f6b2c272358b6e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 30 Oct 2024 15:11:27 +0000 Subject: [PATCH] deploy: 0bea76e2fd92652903b56f3c3f518d19b7a2bfd1 --- search-index.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/search-index.json b/search-index.json index a91a7cb..9861499 100644 --- a/search-index.json +++ b/search-index.json @@ -1 +1 @@ -[{"documents":[{"i":1,"t":"Convergence tests","u":"/openmx/convergence","b":[]},{"i":9,"t":"Resources","u":"/openmx/resources","b":[]},{"i":11,"t":"Bandstructure and DOS of diamond","u":"/openmx/diamond","b":[]},{"i":15,"t":"License","u":"/openmx/license","b":[]},{"i":17,"t":"Orbital decomposition of bandstructure","u":"/openmx/orbital-projection","b":[]},{"i":19,"t":"Spin Orbit Coupling","u":"/openmx/soc","b":[]},{"i":23,"t":"DFT+U calculation","u":"/openmx/dft-u","b":[]},{"i":25,"t":"Bandstructure calculation for 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create input files and run calculations while varying certain parameter: src/convergence/ecut.sh #!/bin/sh NAME=\"ecut\" for CUTOFF in `seq 10 5 50` do cat > ${NAME}_${CUTOFF}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_ecut_${CUTOFF} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff ${CUTOFF} # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 5 5 5 # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${CUTOFF}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${CUTOFF}.in > ${NAME}_${CUTOFF}.out grep -E \"Utot\\s+=\" ${NAME}_${CUTOFF}.out done The script will print out total energy for each cutoff energy used. We can plot the result: import numpy as np import matplotlib.pyplot as plt %matplotlib inline plt.rcParams[\"figure.dpi\"]=150 plt.rcParams[\"figure.facecolor\"]=\"white\" ecut, etot = np.loadtxt(\"../src/convergence/ecut-vs-etot.dat\", unpack=True) plt.plot(ecut, etot, \"o-\", markersize=5) plt.xlabel(\"$E_{cutoff}$ (Ry)\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show() note The cutoff energy in OpenMX is not for the basis set as in plane wave methods, but for the numerical integrations. Therefore the total energy does not have to converge from the upper energy region with respect to the cutoff energy like that of plane wave basis set.","s":"Cutoff energy","u":"/openmx/convergence","h":"#cutoff-energy","p":1},{"i":6,"t":"src/convergence/kgrid.sh #!/bin/sh NAME=\"Kgrid\" for GRID in `seq 2 10` do cat > ${NAME}_${GRID}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_${GRID} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 50 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid ${GRID} ${GRID} ${GRID} # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${GRID}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${GRID}.in > ${NAME}_${GRID}.out grep -E \"Utot\\s+=\" ${NAME}_${GRID}.out done k, etot = np.loadtxt(\"../src/convergence/kgrid-vs-etot.dat\", unpack=True) plt.plot(k, etot, \"o-\", markersize=5) plt.xlabel(\"k_grid\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show()","s":"k-grid density","u":"/openmx/convergence","h":"#k-grid-density","p":1},{"i":8,"t":"src/convergence/alat.sh #!/bin/sh NAME=\"alat\" for ALAT in `seq 5 0.1 6` do ALAT2=$(echo \"scale=7;${ALAT}/2\" | bc) ALAT4=$(echo \"scale=7;${ALAT}/4\" | bc) cat > ${NAME}_${ALAT}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_${ALAT} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 50 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 8 8 8 # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${ALAT}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${ALAT}.in > ${NAME}_${ALAT}.out grep -E \"Utot\\s+=\" ${NAME}_${ALAT}.out done alat, etot = np.loadtxt(\"../src/convergence/alat-vs-etot.dat\", unpack=True) plt.plot(alat, etot, \"o-\", markersize=5) plt.xlabel(\"$a_{lat}$ ($\\\\AA$)\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show()","s":"Lattice constant","u":"/openmx/convergence","h":"#lattice-constant","p":1},{"i":10,"t":"http://www.openmx-square.org","s":"Resources","u":"/openmx/resources","h":"","p":9},{"i":12,"t":"We will run the bandstructure calculation from the OpenMX example file. Here is the input file: src/diamond/diamond.in # File Name System.CurrrentDirectory ./ # default=./ System.Name diamond DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) # Definition of Atomic Species Species.Number 1 # Atoms Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU # SCF or Electronic System scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 150.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # DC|GDC|Cluster|Band scf.Kgrid 7 7 7 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.30 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.700 # default=0.40 scf.Mixing.History 7 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-10 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type nomd # Nomd|Opt|NVE|NVT_VS|NVT_NH MD.maxIter 1 # default=1 MD.TimeStep 1 # default=0.5 (fs) MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr) # Band dispersion # Band.dispersion on # on|off, default=off # if # MO output # MO.fileout off # on|off num.HOMOs 1 # default=2 num.LUMOs 1 # default=2 MO.Nkpoint 2 # default=1 # # DOS and PDOS # Dos.fileout on # on|off, default=off Dos.Erange -25.0 20.0 # default = -20 20 Dos.Kgrid 12 12 12 # default = Kgrid1 Kgrid2 Kgrid3 FermiSurfer.fileout on We can run the calculation using mpirun or submit via job-script: mpirun -np 12 openmx diamond.in > diamond.out Next step is to extract bandstructure data from diamond.Band file: bandgnu13 diamond.Band Finally, we can plot the bandstructure using gnuplot or any plotting program of your choice: gnuplot diamond.GNUBAND","s":"Bandstructure and DOS of diamond","u":"/openmx/diamond","h":"","p":11},{"i":14,"t":"DosMain diamond.Dos.val diamond.Dos.vec It will ask few options interactively. Use of tetrahedron method is suitable. The output file diamond.DOS.Tetrahedron will contain the energy, DOS and integrated DOS columns. While running the DosMain program, you can also choose PDOS for projected density of states for each orbitals.","s":"Density of States (DOS)","u":"/openmx/diamond","h":"#density-of-states-dos","p":11},{"i":16,"t":"This work is licensed under a Creative Commons Attribution 4.0 International License. Any third party materials in this work are not included in the article’s Creative Commons license, and users will need to obtain permission from the respective license holder to reproduce such materials. You are free to: Share — copy and redistribute the material in any medium or format. Adapt — remix, transform, and build upon the material for any purpose, even commercially. Under the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. Notices: No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. To view full copy of this license, visit http://creativecommons.org/licenses/by/4.0/","s":"License","u":"/openmx/license","h":"","p":15},{"i":18,"t":"If you want to decompose the individual orbital contributions on the bandstructure, here are the relevant keywords: src/SiC/SiC_Primitive_BD.in Unfolding.Electronic.Band on # on|off default=off Unfolding.LowerBound -10.0 # default=-10 eV Unfolding.UpperBound 6.0 # default= 10 eV Unfolding.desired_totalnkpt 30 Unfolding.Nkpoint 4 The orbital contributions are saved in {system}.unfold_orb. In case of spin polarized calculation, there will be {system}.unfold_orb{up, dn}. The sequence of the orbitally decomposed spectral weights can be found in {system}.out; look for the section Unfolding calculation for band structure towards the bottom of the file. More details: http://www.openmx-square.org/openmx_man3.9/node168.html","s":"Orbital decomposition of bandstructure","u":"/openmx/orbital-projection","h":"","p":17},{"i":20,"t":"In order to perform fully relativistic calculation: (A) Full relativistic effects can only be applied in non-collinear calculations. scf.SpinPolarization NC # On|Off|NC When the option NC is specified, wave functions are expressed by a two component spinor, and initial spin orientation of each site should be provided: Col Description 1 sequential serial number 2 species name 3 x-coordinate 4 y-coordinate 5 z-coordinate 6 initial occupation for up spin 7 initial occupation for down spin 8 Euler angle, theta, of the magnetic field for spin magnetic moment 9 Euler angle, phi, of the magnetic field for spin magnetic moment. Also, the 8th and 9th are used to generate the initial non-collinear spin charge distribution 10 the Euler angle, theta, of the magnetic field for orbital magnetic moment 11 the Euler angle, phi, of the magnetic field for orbital magnetic moment 12 switch for the constraint schemes specified by the keywords scf.Constraint.NC.Spin and scf.NC.Zeeman.Orbital. 1 means that the constraint is applied, and 0 no constraint. 13 switch for enhancement of orbital polarization in the LDA+U method, on means that the enhancement is made, off means no enhancement. (B) Use jjj-dependent pseudopotential, i.e., it incorporates full relativistic correction. (C) Turn on the soc flag: scf.SpinOrbit.Coupling on # On|Off, default=off","s":"Spin Orbit Coupling","u":"/openmx/soc","h":"","p":19},{"i":22,"t":"Here we compare the bulk and surface electronic structure of topological insulating Bi2Se3. In both cases we consider noncollinear magnetism with spin orbit coupling. In case of slab calculation 10 Å vacuum is introduced among the layers.","s":"Bulk and surface bands for Bi2Se3","u":"/openmx/soc","h":"#bulk-and-surface-bands-for-bi2se3","p":19},{"i":24,"t":"We will calculate the density of states for NiO with and without including Hubbard UUU. We will start from the example input file for NiO (check work directory under OpenMX installation). src/NiO/NiO.in # File Name # System.CurrrentDirectory ./ # default=./ System.Name nio level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (1-3) DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 # Definition of Atomic Species # Species.Number 2 # Atoms # Atoms.Number 4 Atoms.SpeciesAndCoordinates.Unit AU # Ang|AU Atoms.UnitVectors.Unit AU # Ang|AU # SCF or Electronic System # scf.XcType LSDA-CA # LDA|LSDA-CA|GGA-PBE # DFT+U part # scf.Hubbard.U On # On|Off, default=off scf.Hubbard.Occupation dual # onsite|full|dual, default=dual scf.DFTU.Type 2 # 1:Simplified(Dudarev)|2:General, default=1 scf.dc.Type sFLL # sFLL|sAMF|cFLL|cAMF, default=sFLL scf.Slater.Ratio 0.625 # default=0.625 scf.Yukawa off # default=off scf.SpinPolarization On # On|Off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 150.0 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.Kgrid 6 6 6 # means 4x4x4 scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.20 # default=0.30 scf.Min.Mixing.Weight 0.01 # default=0.001 scf.Max.Mixing.Weight 0.30 # default=0.40 scf.Kerker.factor 1.00 # default=1.00 scf.Mixing.History 5 # default=5 scf.Mixing.StartPulay 6 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) # MD or Geometry Optimization # MD.Type nomd # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH MD.maxIter 1 # default=1 MD.TimeStep 0.05 # default=0.5 (fs) MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr) # Band dispersion # Voronoi.Charge on Band.dispersion off # on|off, default=off # if # MO output # MO.fileout off # on|off num.HOMOs 1 # default=1 num.LUMOs 1 # default=1 MO.Nkpoint 1 # default=1 # DOS and LDOS # Dos.fileout on # on|off , default=off Dos.Erange -10.0 10.0 # default = -20 20 Dos.Kgrid 9 9 9 # default = Kgrid1 Kgrid2 Kgrid3 # output Hamiltonian and overlap # HS.fileout off # on|off, default=off note If the initial spin configuration is unpolarized for LDA+U calculations, it is required to provide the switch for enhancement of orbital polarization in the LDA+U method in the last column of Atoms.SpeciesAndCoordinates, on means that the enhancement is made, off means no enhancement. Here we compare the density of states with and without considering electronic correlation. tip If you have difficulty with SCF convergence, you might try scf.Mixing.Type Rmm-Diish which is suitable for the plus U method and the constraint schemes. Find more details here.","s":"DFT+U calculation","u":"/openmx/dft-u","h":"","p":23},{"i":26,"t":"Here we will calculate the bandstructure of silicon. First step is to perform the scf calculation. Here is our input file: src/silicon/silicon.in # File Name System.CurrrentDirectory ./ # default=./ System.Name silicon DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) # Definition of Atomic Species Species.Number 1 # Atoms Atoms.Number 8 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU # SCF or Electronic System scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization off # On|Off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 160.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 7 7 7 # means nk1xnk2xnk3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-8 # default=1.0e-6 (Hartree) Band.dispersion on # on|off, default=off Band.Nkpath 4 We can run the calculation using mpirun or submit via job-script: mpirun -np 12 openmx silicon.in > silicon.out While the calculation is running, you can monitor the convergence by: grep \"dUele\" silicon.out | tail Next step is to extract bandstructure data from silicon.Band file: bandgnu13 silicon.Band Finally, we can plot the bandstructure using gnuplot or any program of your choice: gnuplot silicon.GNUBAND","s":"Bandstructure calculation for silicon","u":"/openmx/silicon","h":"","p":25},{"i":28,"t":"While performing non-colinear magnetic calculations, you will find a file named {system}.nc.xsf in the output directory. You can open this structure file in XCrySDen. XCrySDen Menu: File → Open Structure → Open XSF. Then go to Display menu and select Forces. You may need to adjust scaling for the force vectors, go to Modify → Force Settings and set suitable Length factor. You can change the background color from black from the Palette Menu which is located in the left of File menu. Here is an example output in XCrySDen:","s":"Visualizing Magnetic Moment","u":"/openmx/moment-visualization","h":"","p":27},{"i":30,"t":"Please refer to the OpenMX website for detailed documentations. The installation options will depend on your system architecture and available libraries. I am installing OpenMX version 3.9.9 at one of NUS HPC clusters. Get the source code: wget http://t-ozaki.issp.u-tokyo.ac.jp/openmx3.9.tar.gz wget http://www.openmx-square.org/bugfixed/21Oct17/patch3.9.9.tar.gz tar -zxvf openmx3.9.tar.gz rm openmx3.9.tar.gz mv patch3.9.9.tar.gz openmx3.9/source cd openmx3.9/source tar -zxvf patch3.9.9.tar.gz rm patch3.9.9.tar.gz","s":"Setting up OpenMX","u":"/openmx/","h":"","p":29},{"i":32,"t":"If you already have Intel OneAPI/Math Kernel libraries installed, load the respective modulefiles or set environment variables: module load xe_2015 You may check the necessary environment variables: echo $LD_LIBRARY_PATH echo $MKLROOT env Open the makefile and specify CC, FC, and LIB flags according to your system and libraries. I am using MPI and Intel Math Kernel Libraries. CC = mpicc -O3 -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpif90 -O3 -qopenmp -I${MKLROOT}/include/fftw LIB= -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore warning Currently I found some issues with the Intel license server while using xe_2015 module at NUS HPC clusters. After the module load, you need to export following ENV variable: export \"INTEL_LICENSE_FILE=/app1/centos6.3/Intel/xe_2015/composer_xe_2015.3.187/licenses\" If you have xe_2018 (instead of xe_2015): module load xe_2018 Use following flags: MKLROOT = /opt/intel/mkl CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp LIB= -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore Once you are set, compile and build the executables: make -j8 all make install Compile the DosMain program: make DosMain There is bandgnu13.c in the source directory, which resulted in error. It needs be compiled using gcc: module purge gcc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ Optionally you may add the openmx3.9/work PATH to your .bashrc. export PATH=\"/home/svu/{username}/openmx3.9/work:$PATH\"","s":"Using Intel libraries","u":"/openmx/","h":"#using-intel-libraries","p":29},{"i":34,"t":"You may use below script to download and install 2023.1 version of Intel oneAPI libraries: scripts/intel_oneapi_components_2023.1.sh #!/bin/bash # Installation script for various Intel oneAPI components # INSTALL_PATH=\"/workspaces/compilers\" CWD=${PWD} BUILD_DIR=/tmp cd ${BUILD_DIR} sudo apt update sudo apt install -y --no-install-recommends autoconf gawk gcc g++ make wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/89283df8-c667-47b0-b7e1-c4573e37bd3e/l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh # for custom location: --install-dir ${INSTALL_PATH}/intel # sh ./l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh -a --silent --eula accept rm l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/150e0430-63df-48a0-8469-ecebff0a1858/l_fortran-compiler_p_2023.1.0.46348_offline.sh # sh ./l_fortran-compiler_p_2023.1.0.46348_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_fortran-compiler_p_2023.1.0.46348_offline.sh -a --silent --eula accept rm l_fortran-compiler_p_2023.1.0.46348_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/7dcd261b-12fa-418a-b61b-b3dd4d597466/l_tbb_oneapi_p_2021.9.0.43484_offline.sh # sh ./l_tbb_oneapi_p_2021.9.0.43484_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_tbb_oneapi_p_2021.9.0.43484_offline.sh -a --silent --eula accept rm l_tbb_oneapi_p_2021.9.0.43484_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/l_mpi_oneapi_p_2021.9.0.43482_offline.sh # sh ./l_mpi_oneapi_p_2021.9.0.43482_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_mpi_oneapi_p_2021.9.0.43482_offline.sh -a --silent --eula accept rm l_mpi_oneapi_p_2021.9.0.43482_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/l_onemkl_p_2023.1.0.46342_offline.sh # sh ./l_onemkl_p_2023.1.0.46342_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_onemkl_p_2023.1.0.46342_offline.sh -a --silent --eula accept rm l_onemkl_p_2023.1.0.46342_offline.sh cd ${CWD} Initialize OneAPI/MKL env: source /opt/intel/oneapi/setvars.sh OpenMX makefile configuration: MKLROOT = /opt/intel/oneapi/mkl/2023.1.0 CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl Standalone script to perform OpenMX installations: scripts/openmx_intel.sh #!/bin/bash # this script is not compatible with Bourne shell (sh), use bash instead: # bash openmx_intel.sh # tested on ubuntu 22.04 # exit upon any command failure set -e OPENMX_VER=\"3.9.9\" MINOR_VER=\"3.9\" PATCH_URL=\"https://www.openmx-square.org/bugfixed/21Oct17/patch${OPENMX_VER}.tar.gz\" DOWNLOAD_URL=\"https://www.openmx-square.org/openmx${MINOR_VER}.tar.gz\" INSTALL_DIR=\"${HOME}/openmx/${OPENMX_VER}\" NUM_PROCS=$(nproc) BUILD_DIR=/tmp/_build_$(date +'%Y%m%d%H%M%S') CWD=${PWD} mkdir ${BUILD_DIR} && cd $_ source /opt/intel/oneapi/setvars.sh wget ${DOWNLOAD_URL} tar -xf openmx${MINOR_VER}.tar.gz rm openmx${MINOR_VER}.tar.gz cd openmx${MINOR_VER}/source wget ${PATCH_URL} tar -xf patch${OPENMX_VER}.tar.gz rm patch${OPENMX_VER}.tar.gz mv kpoint.in ../work/ # edit makefile # MKLROOT = /opt/intel/mkl # CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include # FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp # LIB = -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore sed -i 's/^\\s*MKLROOT\\s*=.*/MKLROOT = \\/opt\\/intel\\/oneapi\\/mkl\\/2023\\.1\\.0/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*CC\\s*=.*/CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}\\/include\\/fftw -I${MKLROOT}\\/include/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*FC\\s*=.*/FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*LIB\\s*=.*/LIB = -L${MKLROOT}\\/lib\\/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile make DosMain make -j${NUM_PROCS} all sudo make install mpiicc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ if [ ! -d ${INSTALL_DIR} ]; then mkdir -p ${INSTALL_DIR} fi cd ${CWD} cp -r ${BUILD_DIR}/openmx${MINOR_VER}/* ${INSTALL_DIR} rm -rf ${BUILD_DIR} # run tests (calculations need to be launched from ${INSTALL_DIR}/work) # cd ${INSTALL_DIR}/work # source /opt/intel/oneapi/setvars.sh # export OMP_NUM_THREADS=1 # mpirun -np ${NUM_PROCS} ./openmx -runtest","s":"Install Intel oneAPI","u":"/openmx/","h":"#install-intel-oneapi","p":29},{"i":36,"t":"Alternatively, you may use following script to install OpenMX using GNU libraries: scripts/openmx_gnu.sh #!/bin/bash # this script is not compatible with Bourne shell (sh), use bash instead: # bash openmx_gnu.sh # tested on ubuntu 22.04 # exit upon any command failure set -e OPENMX_VER=\"3.9.9\" MINOR_VER=\"3.9\" PATCH_URL=\"https://www.openmx-square.org/bugfixed/21Oct17/patch${OPENMX_VER}.tar.gz\" DOWNLOAD_URL=\"https://www.openmx-square.org/openmx${MINOR_VER}.tar.gz\" INSTALL_DIR=\"${HOME}/openmx/${OPENMX_VER}\" NUM_PROCS=$(nproc) BUILD_DIR=/tmp/_build_$(date +'%Y%m%d%H%M%S') CWD=${PWD} mkdir ${BUILD_DIR} && cd $_ sudo apt update && sudo apt upgrade -y sudo apt install --no-install-recommends -y \\ autoconf \\ build-essential \\ ca-certificates \\ gfortran \\ libblas3 \\ libopenblas-dev \\ libc6 \\ libfftw3-dev \\ libgcc-s1 \\ liblapack-dev \\ libopenmpi-dev \\ libscalapack-openmpi-dev \\ libelpa-dev \\ wget if ! [ -f /usr/lib/x86_64-linux-gnu/libscalapack.so ] ; then if ! [ -h /usr/lib/x86_64-linux-gnu/libscalapack.so ] ; then sudo ln -s /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so /usr/lib/x86_64-linux-gnu/libscalapack.so fi fi wget ${DOWNLOAD_URL} tar -xf openmx${MINOR_VER}.tar.gz rm openmx${MINOR_VER}.tar.gz cd openmx${MINOR_VER}/source wget ${PATCH_URL} tar -xf patch${OPENMX_VER}.tar.gz rm patch${OPENMX_VER}.tar.gz mv kpoint.in ../work/ # edit makefile # to find specific paths try: apt search fftw3; dpkg -L libfftw3-dev; ompi_info # CC = mpicc -O3 -ffast-math -fcommon -fopenmp # FC = mpif90 -O3 -ffast-math -fallow-argument-mismatch -fopenmp # LIB = -lfftw3 -lmpi -lmpi_mpifh -lscalapack -llapack -lblas -lgfortran sed -i 's/^\\s*CC\\s*=.*/CC = mpicc -O3 -ffast-math -fcommon -fopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i '/^\\s*MKLROOT/d' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*FC\\s*=.*/FC = mpif90 -O3 -ffast-math -fallow-argument-mismatch -fopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*LIB\\s*=.*/LIB = -lfftw3 -lmpi -lmpi_mpifh -lscalapack -llapack -lblas -lgfortran/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile make DosMain make -j${NUM_PROCS} all sudo make install mpicc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ if [ ! -d ${INSTALL_DIR} ]; then mkdir -p ${INSTALL_DIR} fi cp -r ${BUILD_DIR}/openmx${MINOR_VER}/* ${INSTALL_DIR} rm -rf ${BUILD_DIR} # run tests (calculations need to be launched from ${INSTALL_DIR}/work) # cd ${INSTALL_DIR}/work # export OMP_NUM_THREADS=1 # mpirun -np ${NUM_PROCS} ./openmx -runtest cd ${CWD}","s":"Using GNU libraries","u":"/openmx/","h":"#using-gnu-libraries","p":29},{"i":38,"t":"If you like to run tests to verify your installation: cd openmx3.9/work mpirun -np 4 ./openmx -runtest You may compare CPU times with other machines.","s":"Verify installation","u":"/openmx/","h":"#verify-installation","p":29},{"i":40,"t":"Here is a sample PBS job script for NUS HPC cluster: scripts/job.pbs #!/bin/bash #PBS -q parallel12 #PBS -l select=2:ncpus=12:mpiprocs=12:mem=45GB #PBS -j eo #PBS -N openmx-test source /etc/profile.d/rec_modules.sh module load xe_2018 cd $PBS_O_WORKDIR; np=$( cat ${PBS_NODEFILE} | wc -l ); mpirun -np $np -f ${PBS_NODEFILE} openmx input.txt > output.txt Input files, Jupyter notebooks, and other source files used in this tutorial can be found in my GitHub repository: pranabdas/openmx. tip Read through the OpenMX manual for various details. OpenMX viewer can help you choose certain parameters for the input file e.g., basis configuration. You may also consult this reference table. SeeK-path tool can help you build the k-path. The work directory under OpenMX installation contains lots of example files for your reference.","s":"Example PBS 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create input files and run calculations while varying certain parameter: src/convergence/ecut.sh #!/bin/sh NAME=\"ecut\" for CUTOFF in `seq 10 5 50` do cat > ${NAME}_${CUTOFF}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_ecut_${CUTOFF} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff ${CUTOFF} # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 5 5 5 # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${CUTOFF}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${CUTOFF}.in > ${NAME}_${CUTOFF}.out grep -E \"Utot\\s+=\" ${NAME}_${CUTOFF}.out done The script will print out total energy for each cutoff energy used. We can plot the result: import numpy as np import matplotlib.pyplot as plt %matplotlib inline plt.rcParams[\"figure.dpi\"]=150 plt.rcParams[\"figure.facecolor\"]=\"white\" ecut, etot = np.loadtxt(\"../src/convergence/ecut-vs-etot.dat\", unpack=True) plt.plot(ecut, etot, \"o-\", markersize=5) plt.xlabel(\"$E_{cutoff}$ (Ry)\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show() note The cutoff energy in OpenMX is not for the basis set as in plane wave methods, but for the numerical integrations. Therefore the total energy does not have to converge from the upper energy region with respect to the cutoff energy like that of plane wave basis set.","s":"Cutoff energy","u":"/openmx/convergence","h":"#cutoff-energy","p":1},{"i":6,"t":"src/convergence/kgrid.sh #!/bin/sh NAME=\"Kgrid\" for GRID in `seq 2 10` do cat > ${NAME}_${GRID}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_${GRID} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 50 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid ${GRID} ${GRID} ${GRID} # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${GRID}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${GRID}.in > ${NAME}_${GRID}.out grep -E \"Utot\\s+=\" ${NAME}_${GRID}.out done k, etot = np.loadtxt(\"../src/convergence/kgrid-vs-etot.dat\", unpack=True) plt.plot(k, etot, \"o-\", markersize=5) plt.xlabel(\"k_grid\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show()","s":"k-grid density","u":"/openmx/convergence","h":"#k-grid-density","p":1},{"i":8,"t":"src/convergence/alat.sh #!/bin/sh NAME=\"alat\" for ALAT in `seq 5 0.1 6` do ALAT2=$(echo \"scale=7;${ALAT}/2\" | bc) ALAT4=$(echo \"scale=7;${ALAT}/4\" | bc) cat > ${NAME}_${ALAT}.in << EOF System.CurrrentDirectory ./ DATA.PATH /workspaces/openmx3.9/DFT_DATA19 System.Name Si_${ALAT} Species.Number 1 Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization Off # On|Off|NC scf.SpinOrbit.Coupling Off # On|Off, default=off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 50 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 8 8 8 # means 4x4x4 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) EOF echo \"Calculating ${NAME}_${ALAT}\" mpirun -np 4 /workspaces/openmx3.9/work/openmx ${NAME}_${ALAT}.in > ${NAME}_${ALAT}.out grep -E \"Utot\\s+=\" ${NAME}_${ALAT}.out done alat, etot = np.loadtxt(\"../src/convergence/alat-vs-etot.dat\", unpack=True) plt.plot(alat, etot, \"o-\", markersize=5) plt.xlabel(\"$a_{lat}$ ($\\\\AA$)\") plt.ylabel(\"$E_{tot}$ (Ry)\") plt.show()","s":"Lattice constant","u":"/openmx/convergence","h":"#lattice-constant","p":1},{"i":10,"t":"We will calculate the density of states for NiO with and without including Hubbard UUU. We will start from the example input file for NiO (check work directory under OpenMX installation). src/NiO/NiO.in # File Name # System.CurrrentDirectory ./ # default=./ System.Name nio level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (1-3) DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 # Definition of Atomic Species # Species.Number 2 # Atoms # Atoms.Number 4 Atoms.SpeciesAndCoordinates.Unit AU # Ang|AU Atoms.UnitVectors.Unit AU # Ang|AU # SCF or Electronic System # scf.XcType LSDA-CA # LDA|LSDA-CA|GGA-PBE # DFT+U part # scf.Hubbard.U On # On|Off, default=off scf.Hubbard.Occupation dual # onsite|full|dual, default=dual scf.DFTU.Type 2 # 1:Simplified(Dudarev)|2:General, default=1 scf.dc.Type sFLL # sFLL|sAMF|cFLL|cAMF, default=sFLL scf.Slater.Ratio 0.625 # default=0.625 scf.Yukawa off # default=off scf.SpinPolarization On # On|Off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 150.0 # default=150 (Ry) scf.maxIter 200 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.Kgrid 6 6 6 # means 4x4x4 scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.20 # default=0.30 scf.Min.Mixing.Weight 0.01 # default=0.001 scf.Max.Mixing.Weight 0.30 # default=0.40 scf.Kerker.factor 1.00 # default=1.00 scf.Mixing.History 5 # default=5 scf.Mixing.StartPulay 6 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) # MD or Geometry Optimization # MD.Type nomd # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH MD.maxIter 1 # default=1 MD.TimeStep 0.05 # default=0.5 (fs) MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr) # Band dispersion # Voronoi.Charge on Band.dispersion off # on|off, default=off # if # MO output # MO.fileout off # on|off num.HOMOs 1 # default=1 num.LUMOs 1 # default=1 MO.Nkpoint 1 # default=1 # DOS and LDOS # Dos.fileout on # on|off , default=off Dos.Erange -10.0 10.0 # default = -20 20 Dos.Kgrid 9 9 9 # default = Kgrid1 Kgrid2 Kgrid3 # output Hamiltonian and overlap # HS.fileout off # on|off, default=off note If the initial spin configuration is unpolarized for LDA+U calculations, it is required to provide the switch for enhancement of orbital polarization in the LDA+U method in the last column of Atoms.SpeciesAndCoordinates, on means that the enhancement is made, off means no enhancement. Here we compare the density of states with and without considering electronic correlation. tip If you have difficulty with SCF convergence, you might try scf.Mixing.Type Rmm-Diish which is suitable for the plus U method and the constraint schemes. Find more details here.","s":"DFT+U calculation","u":"/openmx/dft-u","h":"","p":9},{"i":12,"t":"This work is licensed under a Creative Commons Attribution 4.0 International License. Any third party materials in this work are not included in the article’s Creative Commons license, and users will need to obtain permission from the respective license holder to reproduce such materials. You are free to: Share — copy and redistribute the material in any medium or format. Adapt — remix, transform, and build upon the material for any purpose, even commercially. Under the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. Notices: No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. To view full copy of this license, visit http://creativecommons.org/licenses/by/4.0/","s":"License","u":"/openmx/license","h":"","p":11},{"i":14,"t":"http://www.openmx-square.org","s":"Resources","u":"/openmx/resources","h":"","p":13},{"i":16,"t":"If you want to decompose the individual orbital contributions on the bandstructure, here are the relevant keywords: src/SiC/SiC_Primitive_BD.in Unfolding.Electronic.Band on # on|off default=off Unfolding.LowerBound -10.0 # default=-10 eV Unfolding.UpperBound 6.0 # default= 10 eV Unfolding.desired_totalnkpt 30 Unfolding.Nkpoint 4 The orbital contributions are saved in {system}.unfold_orb. In case of spin polarized calculation, there will be {system}.unfold_orb{up, dn}. The sequence of the orbitally decomposed spectral weights can be found in {system}.out; look for the section Unfolding calculation for band structure towards the bottom of the file. More details: http://www.openmx-square.org/openmx_man3.9/node168.html","s":"Orbital decomposition of bandstructure","u":"/openmx/orbital-projection","h":"","p":15},{"i":18,"t":"We will run the bandstructure calculation from the OpenMX example file. Here is the input file: src/diamond/diamond.in # File Name System.CurrrentDirectory ./ # default=./ System.Name diamond DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) # Definition of Atomic Species Species.Number 1 # Atoms Atoms.Number 2 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU # SCF or Electronic System scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 150.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # DC|GDC|Cluster|Band scf.Kgrid 7 7 7 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.30 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.700 # default=0.40 scf.Mixing.History 7 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-10 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type nomd # Nomd|Opt|NVE|NVT_VS|NVT_NH MD.maxIter 1 # default=1 MD.TimeStep 1 # default=0.5 (fs) MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr) # Band dispersion # Band.dispersion on # on|off, default=off # if # MO output # MO.fileout off # on|off num.HOMOs 1 # default=2 num.LUMOs 1 # default=2 MO.Nkpoint 2 # default=1 # # DOS and PDOS # Dos.fileout on # on|off, default=off Dos.Erange -25.0 20.0 # default = -20 20 Dos.Kgrid 12 12 12 # default = Kgrid1 Kgrid2 Kgrid3 FermiSurfer.fileout on We can run the calculation using mpirun or submit via job-script: mpirun -np 12 openmx diamond.in > diamond.out Next step is to extract bandstructure data from diamond.Band file: bandgnu13 diamond.Band Finally, we can plot the bandstructure using gnuplot or any plotting program of your choice: gnuplot diamond.GNUBAND","s":"Bandstructure and DOS of diamond","u":"/openmx/diamond","h":"","p":17},{"i":20,"t":"DosMain diamond.Dos.val diamond.Dos.vec It will ask few options interactively. Use of tetrahedron method is suitable. The output file diamond.DOS.Tetrahedron will contain the energy, DOS and integrated DOS columns. While running the DosMain program, you can also choose PDOS for projected density of states for each orbitals.","s":"Density of States (DOS)","u":"/openmx/diamond","h":"#density-of-states-dos","p":17},{"i":22,"t":"In order to perform fully relativistic calculation: (A) Full relativistic effects can only be applied in non-collinear calculations. scf.SpinPolarization NC # On|Off|NC When the option NC is specified, wave functions are expressed by a two component spinor, and initial spin orientation of each site should be provided: Col Description 1 sequential serial number 2 species name 3 x-coordinate 4 y-coordinate 5 z-coordinate 6 initial occupation for up spin 7 initial occupation for down spin 8 Euler angle, theta, of the magnetic field for spin magnetic moment 9 Euler angle, phi, of the magnetic field for spin magnetic moment. Also, the 8th and 9th are used to generate the initial non-collinear spin charge distribution 10 the Euler angle, theta, of the magnetic field for orbital magnetic moment 11 the Euler angle, phi, of the magnetic field for orbital magnetic moment 12 switch for the constraint schemes specified by the keywords scf.Constraint.NC.Spin and scf.NC.Zeeman.Orbital. 1 means that the constraint is applied, and 0 no constraint. 13 switch for enhancement of orbital polarization in the LDA+U method, on means that the enhancement is made, off means no enhancement. (B) Use jjj-dependent pseudopotential, i.e., it incorporates full relativistic correction. (C) Turn on the soc flag: scf.SpinOrbit.Coupling on # On|Off, default=off","s":"Spin Orbit Coupling","u":"/openmx/soc","h":"","p":21},{"i":24,"t":"Here we compare the bulk and surface electronic structure of topological insulating Bi2Se3. In both cases we consider noncollinear magnetism with spin orbit coupling. In case of slab calculation 10 Å vacuum is introduced among the layers.","s":"Bulk and surface bands for Bi2Se3","u":"/openmx/soc","h":"#bulk-and-surface-bands-for-bi2se3","p":21},{"i":26,"t":"Here we will calculate the bandstructure of silicon. First step is to perform the scf calculation. Here is our input file: src/silicon/silicon.in # File Name System.CurrrentDirectory ./ # default=./ System.Name silicon DATA.PATH /home/svu/slspkd/openmx3.9/DFT_DATA19 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) # Definition of Atomic Species Species.Number 1 # Atoms Atoms.Number 8 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.UnitVectors.Unit Ang # Ang|AU # SCF or Electronic System scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW scf.SpinPolarization off # On|Off scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 160.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # Recursion|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 7 7 7 # means nk1xnk2xnk3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 15 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.criterion 1.0e-8 # default=1.0e-6 (Hartree) Band.dispersion on # on|off, default=off Band.Nkpath 4 We can run the calculation using mpirun or submit via job-script: mpirun -np 12 openmx silicon.in > silicon.out While the calculation is running, you can monitor the convergence by: grep \"dUele\" silicon.out | tail Next step is to extract bandstructure data from silicon.Band file: bandgnu13 silicon.Band Finally, we can plot the bandstructure using gnuplot or any program of your choice: gnuplot silicon.GNUBAND","s":"Bandstructure calculation for silicon","u":"/openmx/silicon","h":"","p":25},{"i":28,"t":"While performing non-colinear magnetic calculations, you will find a file named {system}.nc.xsf in the output directory. You can open this structure file in XCrySDen. XCrySDen Menu: File → Open Structure → Open XSF. Then go to Display menu and select Forces. You may need to adjust scaling for the force vectors, go to Modify → Force Settings and set suitable Length factor. You can change the background color from black from the Palette Menu which is located in the left of File menu. Here is an example output in XCrySDen:","s":"Visualizing Magnetic Moment","u":"/openmx/moment-visualization","h":"","p":27},{"i":30,"t":"Please refer to the OpenMX website for detailed documentations. The installation options will depend on your system architecture and available libraries. I am installing OpenMX version 3.9.9 at one of NUS HPC clusters. Get the source code: wget http://t-ozaki.issp.u-tokyo.ac.jp/openmx3.9.tar.gz wget http://www.openmx-square.org/bugfixed/21Oct17/patch3.9.9.tar.gz tar -zxvf openmx3.9.tar.gz rm openmx3.9.tar.gz mv patch3.9.9.tar.gz openmx3.9/source cd openmx3.9/source tar -zxvf patch3.9.9.tar.gz rm patch3.9.9.tar.gz","s":"Setting up OpenMX","u":"/openmx/","h":"","p":29},{"i":32,"t":"If you already have Intel OneAPI/Math Kernel libraries installed, load the respective modulefiles or set environment variables: module load xe_2015 You may check the necessary environment variables: echo $LD_LIBRARY_PATH echo $MKLROOT env Open the makefile and specify CC, FC, and LIB flags according to your system and libraries. I am using MPI and Intel Math Kernel Libraries. CC = mpicc -O3 -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpif90 -O3 -qopenmp -I${MKLROOT}/include/fftw LIB= -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore warning Currently I found some issues with the Intel license server while using xe_2015 module at NUS HPC clusters. After the module load, you need to export following ENV variable: export \"INTEL_LICENSE_FILE=/app1/centos6.3/Intel/xe_2015/composer_xe_2015.3.187/licenses\" If you have xe_2018 (instead of xe_2015): module load xe_2018 Use following flags: MKLROOT = /opt/intel/mkl CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp LIB= -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore Once you are set, compile and build the executables: make -j8 all make install Compile the DosMain program: make DosMain There is bandgnu13.c in the source directory, which resulted in error. It needs be compiled using gcc: module purge gcc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ Optionally you may add the openmx3.9/work PATH to your .bashrc. export PATH=\"/home/svu/{username}/openmx3.9/work:$PATH\"","s":"Using Intel libraries","u":"/openmx/","h":"#using-intel-libraries","p":29},{"i":34,"t":"You may use below script to download and install 2023.1 version of Intel oneAPI libraries: scripts/intel_oneapi_components_2023.1.sh #!/bin/bash # Installation script for various Intel oneAPI components # INSTALL_PATH=\"/workspaces/compilers\" CWD=${PWD} BUILD_DIR=/tmp cd ${BUILD_DIR} sudo apt update sudo apt install -y --no-install-recommends autoconf gawk gcc g++ make wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/89283df8-c667-47b0-b7e1-c4573e37bd3e/l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh # for custom location: --install-dir ${INSTALL_PATH}/intel # sh ./l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh -a --silent --eula accept rm l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/150e0430-63df-48a0-8469-ecebff0a1858/l_fortran-compiler_p_2023.1.0.46348_offline.sh # sh ./l_fortran-compiler_p_2023.1.0.46348_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_fortran-compiler_p_2023.1.0.46348_offline.sh -a --silent --eula accept rm l_fortran-compiler_p_2023.1.0.46348_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/7dcd261b-12fa-418a-b61b-b3dd4d597466/l_tbb_oneapi_p_2021.9.0.43484_offline.sh # sh ./l_tbb_oneapi_p_2021.9.0.43484_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_tbb_oneapi_p_2021.9.0.43484_offline.sh -a --silent --eula accept rm l_tbb_oneapi_p_2021.9.0.43484_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/l_mpi_oneapi_p_2021.9.0.43482_offline.sh # sh ./l_mpi_oneapi_p_2021.9.0.43482_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_mpi_oneapi_p_2021.9.0.43482_offline.sh -a --silent --eula accept rm l_mpi_oneapi_p_2021.9.0.43482_offline.sh wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/l_onemkl_p_2023.1.0.46342_offline.sh # sh ./l_onemkl_p_2023.1.0.46342_offline.sh -a --silent --eula accept --install-dir ${INSTALL_PATH}/intel sudo sh ./l_onemkl_p_2023.1.0.46342_offline.sh -a --silent --eula accept rm l_onemkl_p_2023.1.0.46342_offline.sh cd ${CWD} Initialize OneAPI/MKL env: source /opt/intel/oneapi/setvars.sh OpenMX makefile configuration: MKLROOT = /opt/intel/oneapi/mkl/2023.1.0 CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl Standalone script to perform OpenMX installations: scripts/openmx_intel.sh #!/bin/bash # this script is not compatible with Bourne shell (sh), use bash instead: # bash openmx_intel.sh # tested on ubuntu 22.04 # exit upon any command failure set -e OPENMX_VER=\"3.9.9\" MINOR_VER=\"3.9\" PATCH_URL=\"https://www.openmx-square.org/bugfixed/21Oct17/patch${OPENMX_VER}.tar.gz\" DOWNLOAD_URL=\"https://www.openmx-square.org/openmx${MINOR_VER}.tar.gz\" INSTALL_DIR=\"${HOME}/openmx/${OPENMX_VER}\" NUM_PROCS=$(nproc) BUILD_DIR=/tmp/_build_$(date +'%Y%m%d%H%M%S') CWD=${PWD} mkdir ${BUILD_DIR} && cd $_ source /opt/intel/oneapi/setvars.sh wget ${DOWNLOAD_URL} tar -xf openmx${MINOR_VER}.tar.gz rm openmx${MINOR_VER}.tar.gz cd openmx${MINOR_VER}/source wget ${PATCH_URL} tar -xf patch${OPENMX_VER}.tar.gz rm patch${OPENMX_VER}.tar.gz mv kpoint.in ../work/ # edit makefile # MKLROOT = /opt/intel/mkl # CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -I${MKLROOT}/include # FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp # LIB = -L${MKLROOT}/include/fftw -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lifcore sed -i 's/^\\s*MKLROOT\\s*=.*/MKLROOT = \\/opt\\/intel\\/oneapi\\/mkl\\/2023\\.1\\.0/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*CC\\s*=.*/CC = mpiicc -O3 -xHOST -ip -no-prec-div -qopenmp -I${MKLROOT}\\/include\\/fftw -I${MKLROOT}\\/include/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*FC\\s*=.*/FC = mpiifort -O3 -xHOST -ip -no-prec-div -qopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*LIB\\s*=.*/LIB = -L${MKLROOT}\\/lib\\/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lifcore -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile make DosMain make -j${NUM_PROCS} all sudo make install mpiicc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ if [ ! -d ${INSTALL_DIR} ]; then mkdir -p ${INSTALL_DIR} fi cd ${CWD} cp -r ${BUILD_DIR}/openmx${MINOR_VER}/* ${INSTALL_DIR} rm -rf ${BUILD_DIR} # run tests (calculations need to be launched from ${INSTALL_DIR}/work) # cd ${INSTALL_DIR}/work # source /opt/intel/oneapi/setvars.sh # export OMP_NUM_THREADS=1 # mpirun -np ${NUM_PROCS} ./openmx -runtest","s":"Install Intel oneAPI","u":"/openmx/","h":"#install-intel-oneapi","p":29},{"i":36,"t":"Alternatively, you may use following script to install OpenMX using GNU libraries: scripts/openmx_gnu.sh #!/bin/bash # this script is not compatible with Bourne shell (sh), use bash instead: # bash openmx_gnu.sh # tested on ubuntu 22.04 # exit upon any command failure set -e OPENMX_VER=\"3.9.9\" MINOR_VER=\"3.9\" PATCH_URL=\"https://www.openmx-square.org/bugfixed/21Oct17/patch${OPENMX_VER}.tar.gz\" DOWNLOAD_URL=\"https://www.openmx-square.org/openmx${MINOR_VER}.tar.gz\" INSTALL_DIR=\"${HOME}/openmx/${OPENMX_VER}\" NUM_PROCS=$(nproc) BUILD_DIR=/tmp/_build_$(date +'%Y%m%d%H%M%S') CWD=${PWD} mkdir ${BUILD_DIR} && cd $_ sudo apt update && sudo apt upgrade -y sudo apt install --no-install-recommends -y \\ autoconf \\ build-essential \\ ca-certificates \\ gfortran \\ libblas3 \\ libopenblas-dev \\ libc6 \\ libfftw3-dev \\ libgcc-s1 \\ liblapack-dev \\ libopenmpi-dev \\ libscalapack-openmpi-dev \\ libelpa-dev \\ wget if ! [ -f /usr/lib/x86_64-linux-gnu/libscalapack.so ] ; then if ! [ -h /usr/lib/x86_64-linux-gnu/libscalapack.so ] ; then sudo ln -s /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so /usr/lib/x86_64-linux-gnu/libscalapack.so fi fi wget ${DOWNLOAD_URL} tar -xf openmx${MINOR_VER}.tar.gz rm openmx${MINOR_VER}.tar.gz cd openmx${MINOR_VER}/source wget ${PATCH_URL} tar -xf patch${OPENMX_VER}.tar.gz rm patch${OPENMX_VER}.tar.gz mv kpoint.in ../work/ # edit makefile # to find specific paths try: apt search fftw3; dpkg -L libfftw3-dev; ompi_info # CC = mpicc -O3 -ffast-math -fcommon -fopenmp # FC = mpif90 -O3 -ffast-math -fallow-argument-mismatch -fopenmp # LIB = -lfftw3 -lmpi -lmpi_mpifh -lscalapack -llapack -lblas -lgfortran sed -i 's/^\\s*CC\\s*=.*/CC = mpicc -O3 -ffast-math -fcommon -fopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i '/^\\s*MKLROOT/d' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*FC\\s*=.*/FC = mpif90 -O3 -ffast-math -fallow-argument-mismatch -fopenmp/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile sed -i 's/^\\s*LIB\\s*=.*/LIB = -lfftw3 -lmpi -lmpi_mpifh -lscalapack -llapack -lblas -lgfortran/' ${BUILD_DIR}/openmx${MINOR_VER}/source/makefile make DosMain make -j${NUM_PROCS} all sudo make install mpicc bandgnu13.c -lm -o bandgnu13 cp bandgnu13 ../work/ if [ ! -d ${INSTALL_DIR} ]; then mkdir -p ${INSTALL_DIR} fi cp -r ${BUILD_DIR}/openmx${MINOR_VER}/* ${INSTALL_DIR} rm -rf ${BUILD_DIR} # run tests (calculations need to be launched from ${INSTALL_DIR}/work) # cd ${INSTALL_DIR}/work # export OMP_NUM_THREADS=1 # mpirun -np ${NUM_PROCS} ./openmx -runtest cd ${CWD}","s":"Using GNU libraries","u":"/openmx/","h":"#using-gnu-libraries","p":29},{"i":38,"t":"If you like to run tests to verify your installation: cd openmx3.9/work mpirun -np 4 ./openmx -runtest You may compare CPU times with other machines.","s":"Verify installation","u":"/openmx/","h":"#verify-installation","p":29},{"i":40,"t":"Here is a sample PBS job script for NUS HPC cluster: scripts/job.pbs #!/bin/bash #PBS -q parallel12 #PBS -l select=2:ncpus=12:mpiprocs=12:mem=45GB #PBS -j eo #PBS -N openmx-test source /etc/profile.d/rec_modules.sh module load xe_2018 cd $PBS_O_WORKDIR; np=$( cat ${PBS_NODEFILE} | wc -l ); mpirun -np $np -f ${PBS_NODEFILE} openmx input.txt > output.txt Input files, Jupyter notebooks, and other source files used in this tutorial can be found in my GitHub repository: pranabdas/openmx. tip Read through the OpenMX manual for various details. OpenMX viewer can help you choose certain parameters for the input file e.g., basis configuration. You may also consult this reference table. SeeK-path tool can help you build the k-path. The work directory under OpenMX installation contains lots of example files for your reference.","s":"Example PBS 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