Profess@Quantum-ESPRESSO README
This page provides installation and usage notes for the 2014 version of the Profess@Quantum-ESPRESSO interface.
Download the original plain-text README
README
Profess@Quantum-Espresso
Univ. Florida OFDFT group
Last revised: 20 Nov 2014 (v7d)
I. Description
==============
This package provides patches to build the Profess@Quantum-ESPRESSO interface
and modified version of Profess.
Authors: Valentin V. Karasiev <vkarasev@qtp.ufl.edu>, Travis Sjostrom <sjostrom@qtp.ufl.edu),
Sam Trickey <trickey@qtp.ufl.edu>
Licensure: GNU GPL
Modifications of Profess 2.0 include:
-------------------------------------
- Implementation of GGA zero-T kinetic energy functionals: VT84F (at T=0),
mcPBE2, PBETW.
- Finite-T non-interacting free-energy functionals: VT84F, KST2, APBEF
(based on zero-T APBEK), PBETWF, and Thomas-Fermi
- Implementation of XC free-energy functionals: KSDT restricted path integral
Monte-Carlo (RPIMC) based (Ref. 5 below) and Perrot-Dharma-wardana
(both 1984 and 2000)
Profess@Quantum-ESPRESSO interface includes:
--------------------------------------------
- Software coupling Profess and Quantum ESPRESSO which permits use of OFDFT
forces from Profess to drive molecular dynamics simulations in Quantum
ESPRESSO.
- Modified part of Kohn-Sham code PWscf includes implementation of the same
XC free-energy functionals as listed above: KSDT restricted path integral
Monte-Carlo (RPIMC) based, Perrot-Dharma-wardana (1984 and 2000).
II. Main references:
====================
-1- "Born – Oppenheimer interatomic forces from simple,
local kinetic energy density functionals", V.V. Karasiev, S.B. Trickey,
and Frank E. Harris, Journal of Computer-Aided Materials Design 13,
111–129 (2006).
-2- "Properties of constraint-based single-point approximate kinetic energy
functionals", V. V. Karasiev, R. S. Jones, S. B. Trickey, and
Frank E. Harris, Physical Review B 80, 245120 (2009); erratum Physical Review
B 87, 239902 (2013)
-3- "Generalized-gradient-approximation noninteracting free-energy functionals
for orbital-free density functional calculations", Valentin V. Karasiev,
Travis Sjostrom, and S. B. Trickey, Physical Review B 86, 115101 (2012).
-4- "Nonempirical generalized gradient approximation free-energy functional
for orbital-free simulations", Valentin V. Karasiev, Debajit Chakraborty,
Olga A. Shukruto, and S. B. Trickey, Physical Review B 88, 161108(R)
(2013).
-5- "Accurate homogeneous electron gas exchange-correlation free energy for
local spin-density calculations", Valentin V. Karasiev, Travis Sjostrom,
James Dufty, and S.B. Trickey, Physical Review Letters 112, 076403 (2014).
-6- "Innovations in finite-temperature density functionals", V.V. Karasiev,
T. Sjostrom, D.Chakraborty, J.W. Dufty, F.E. Harris, K. Runge, and S.B.
Trickey, chapter in "Computational Challenges in Warm Dense Matter", F.
Graziani et al. eds., Springer Verlag (2014); 61-75.
-7- "Finite-temperature orbital-free DFT molecular dynamics: Coupling Profess
and Quantum Espresso", V.V. Karasiev, T. Sjostrom, and S.B. Trickey,
Computer Physics Communications 185, 3240-3249 (2014).
- See also references in the original Profess and Quantum-Espresso packages.
- Also see http://www.qtp.ufl.edu/ofdft for occasional updates, bug fixes, etc.
III. Pre-requisites and convention
==================================
Linux with Bourne-again shell (bash)
Intel ifort and icc compilers
Convention: in paths, the tilde (~) indicates (and is translated by bash as)
your home directory:
~/OFQE is /home/<user_name>/OFQE
If you install the package in a different directory, change "~" to <your_local_path>
In any case, in the procedures below change
./configure --prefix=/home/vkarasev/OFQE
to
./configure --prefix=<your_local_path>/OFQE
IV. Distribution and File list
==============================
Distribution consists of this README and a tarball, ProfAtQE.yyyy.mm.dd.tgz
containing the following files, all in a directory named OFQE.
patches/espresso-5.0.3-5.0.3m.diff Patch for Quantum ESPRESSO v.5.0.3
patches/PROFESS2-PROFESS2m4.diff Patch for Profess v.2.0
patches/fftw-2.1.5-profftw-2.1.5.diff Patch for fftw-2.1.5
examples-OFDFT Examples to run OFDFT Profess
examples-PROFESS@QE Examples to run Profess@Quantum-ESPRESSO
PP Directory with pseudopotential files,
PP/recpot - local in reciprocal space,
PP/UPF - local and PAW (in UPF format)
transferable to high material density.
tools Directory with script(s) for extracting
key output
download Directory (empty) for downloading 3rd party
sources
V. Download
===========
Download the following files and place them in the directory ~/OFQE/download :
- FFTW 2.1.5 (fftw-2.1.5.tar.gz file) from here: http://www.fftw.org/
or use direct link: http://www.fftw.org/fftw-2.1.5.tar.gz
- PROFESS 2.0 (AEBN_v2_0 catalog ID) from here: http://www.cpc.cs.qub.ac.uk/
- Quantum ESPRESSO 5.0.2 (espresso-5.0.2.tar.gz file) including PHonon as
well (PHonon-5.0.2.tar.gz) and patch for v.5.0.2 - CORRECTED on May 6- 2013
(espresso-5.0.2-5.0.3.diff file) from here:
http://www.qe-forge.org/gf/project/q-e/frs/?action=FrsReleaseBrowse&frs_package_id=18
direct links to the files:
http://www.qe-forge.org/gf/download/frsrelease/116/403/espresso-5.0.2.tar.gz
http://www.qe-forge.org/gf/download/frsrelease/116/405/PHonon-5.0.2.tar.gz
http://www.qe-forge.org/gf/download/frsrelease/128/435/espresso-5.0.2-5.0.3.diff
VI. Applying patches
====================
Place distribution file ProfAtQE.yyyy.mm.dd.tgz in the installation directory
(home directory in our case), unpack all files:
tar xzvf ProfAtQE.yyyy.mm.dd.tgz
and apply patches:
cd ~/OFQE
tar xzvf download/fftw-2.1.5.tar.gz
tar xzvf download/aebn_v2_0.tar.gz
tar xzvf download/espresso-5.0.2.tar.gz
tar xzvf download/PHonon-5.0.2.tar.gz
mv PHonon espresso-5.0.2
mv espresso-5.0.2 espresso-5.0.3m
cd espresso-5.0.3m
patch -p1 < ../download/espresso-5.0.2-5.0.3.diff
patch -p1 < ../patches/espresso-5.0.3-5.0.3m.diff
cd ..
mv PROFESS2 PROFESS2m4
cd PROFESS2m4
patch -p1 < ../patches/PROFESS2-PROFESS2m4.diff
cd ..
mv fftw-2.1.5 profftw-2.1.5
cd profftw-2.1.5
patch -p1 < ../patches/fftw-2.1.5-profftw-2.1.5.diff
VII. Serial compilation
=======================
A. Compile profftw library:
---------------------------
cd ~/OFQE/profftw-2.1.5
./configure --prefix=/home/vkarasev/OFQE/profftw-2.1.5 CC=icc F77=ifort
make
make install
B. Compile OFDFT library:
-------------------------
cd ~/OFQE/PROFESS2m4
rm -rf Makefile
ln -s Makefile_intel_2_lib Makefile
make clean
make
C. Compile Profess@Quantum-ESSPRESSO interface:
-----------------------------------------------
cd ~/OFQE/espresso-5.0.3m
./configure CC=icc F77=ifort
cd PW/src
rm -rf Makefile
ln -s Makefile_WithOFDFT_seq Makefile
cd ../..
(**option: make clean)
make pw
D. Compilation of modified PROFESS as a stand-alone package (recommended):
--------------------------------------------------------------------------
cd ~/OFQE/PROFESS2m4
rm -f Makefile
ln -s Makefile_intel_2 Makefile
(**option: make clean)
make
If you intend only serial compilation, skip to Sect. IX. "Run Examples ..."
VIII. Parallel compilation
==========================
(Be sure that modules required for parallel compilation/execution
like openmpi etc are loaded, e.g. "module load intel openmpi" )
A. Compile profftw library:
---------------------------
cd ~/OFQE/profftw-2.1.5
./configure --prefix=/home/vkarasev/OFQE/profftw-2.1.5_mpi CC=mpicc F77=mpif77 --enable-mpi
make
make install
B. Compile OFDFT library:
-------------------------
cd ~/OFQE/PROFESS2m4
rm -rf Makefile
ln -s Makefile_intel_2_lib Makefile
(**optional: make clean)
make parallel
C. Compile Profess@Quantum-ESSPRESSO:
-------------------------------------
cd ~/OFQE/espresso-5.0.3m
./configure
cd PW/src
rm -rf Makefile
ln -s Makefile_WithOFDFT_par Makefile
cd ../..
(**optional: make clean)
make pw
D. Compilation of PROFESS:
--------------------------
cd ~/OFQE/PROFESS2m4
rm -f Makefile
ln -s Makefile_intel_2 Makefile
(**optional: make clean)
make parallel
IX. Run examples with modified Profess
======================================
remark:
a stack size change may be required. Do
ulimit -s unlimited
----------------------------------------------------------------
A. fcc-Al static lattice (Profess alone) calculation of energy
vs. lattice constant for the VT84F free-energy and the LDA XC
functionals at electronic temperature T_el=100K:
----------------------------------------------------------------
cd ~/OFQE/examples-OFDFT/Al.--locmodreg_rc1.15-qtpHA/scripts
sh Al4-fcc_1X1X1r0.sh
extract data:
cd ../Al-fcc_1X1X1r0-lda-stn-500eV-two-T100K
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh VT84F+XC.T100
and find results in the V-E-P-Ax-Rho.VT84F+XC.T100.data file.
------------------------------------------------------------
B. sc-H static lattice (Profess alone) calculation of energy
vs. lattice constant for the VT84F, APBEF, PBETWF, KST2,
SGA and TF free-energy and the LDA XC functionals
at electronic temperature T_el=100K:
------------------------------------------------------------
cd ~/OFQE/examples-OFDFT/H.pz-locmodreg_rc0.25-qtp/scripts
sh H-sc_2X2X2r0.sh
remark:
this example took a few minutes wall clock on a single 2.67 GHz I7 core
of an 8-core system with no other significant load.
extract data:
cd ../H-sc_2X2X2r0-lda-stn-4000eV-odd-T100K
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh VT84F+XC.T100
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh APBEF+XC.T100
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh PBETWF+XC.T100
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh KST2+XC.T100
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh TSGA+XC.T100
sh ../../../tools/extr-V-E-P-Ax-Rho-profess.sh TTF+XC.T100
find results here:
V-E-P-Ax-Rho.VT84F+XC.T100.data
V-E-P-Ax-Rho.APBEF+XC.T100.data
V-E-P-Ax-Rho.PBETWF+XC.T100.data
V-E-P-Ax-Rho.KST2+XC.T100.data
V-E-P-Ax-Rho.TSGA+XC.T100.data
V-E-P-Ax-Rho.TTF+XC.T100.data
X. Run OF-DFT molecular dynamics with Profess@Quantum-ESPRESSO
==============================================================
--------------------------------------------------------------
A. Hydrogen, 128 atoms, Rho_H=0.983 g/cm^3, T=125000K,
OFDFT=TF(Fs)+KSDT(XC), 100 MD steps
starting from simple-cubic positions:
--------------------------------------------------------------
cd ~/OFQE/examples-PROFESS@QE/H128.md.verl.andr.OFDFT/scripts
sh md-H128.TTF.R0.983.T125kK.sh
cd ../TTF+ksdt.ecut3000.R0.983.T125000.stn.nr20
remarks:
during calculation, most recent MD step can be monitored in files
pos.last (top line), ofdft.out, and H.*.out
this example took 33:22 (33min22sec) wall clock on a single 2.67 GHz I7 core
of an 8-core system with no other significant load.
find results here:
H.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.out
modified QE output
md.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.xyz
cartesian fractional positions of all atoms at each MD step
ofdft.err
Profess error messages if any (should be empty)
ofdft.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.out
Profess (as UF modified) output
pwscf.msd.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.dat
QE mean square displacements
pwscf.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.md
QE most recent MD step information
pwscf.rdf.R0.983.T125000.TTF+ksdt.ecut3000.NMDSTEP100.dt56as.nr20.dat
QE radial distribution function
Remark: though the sample output for MD simulation examples is provided,
the reproduced data should be in agreement on the first MD step only
due to the use of random number generator during MD simulations.
------------------------------------------------------------------
B. Hydrogen, 128 atoms, Rho_H=0.983 g/cm^3, T=125000K,
OFDFT=VT84F(Fs)+KSDT(XC), [Refs. 4, 5], 10 MD steps
starting from the last configuration in previous
simulation stored in pos.last-TTF.R0.983.T125000.101steps file:
------------------------------------------------------------------
cd ~/OFQE/examples-PROFESS@QE/H128.md.verl.andr.OFDFT/scripts
sh md-H128.VT84F.R0.983.T125kK.sh
cd ../VT84F+ksdt.ecut3000.R0.983.T125000.stn.nr20
remark:
this example took 24:54 wall clock on a single 2.67 GHz I7 core
of an 8-core system with no other significant load.
find results here:
files analogous with those in preceding example
-------------------------------------------------------------------
C. Hydrogen, 128 atoms, Rho_H=0.983 g/cm^3, T=62500K,
Kohn-Sham MD with T-dependent XC (KS+KSDT(XC)), [Ref. 5], 5 MD steps
starting from the last configuration in OFDFT=TF(Fs)+KSDT(XC)
simulation stored in pos.last-TTF.R0.983.T125000.101steps file:
-------------------------------------------------------------------
cd ~/OFQE/examples-PROFESS@QE/H128.md.verl.andr.OFDFT/scripts
sh md-H128.KS.R0.983.T62.5kK.sh
cd ../H128-R0.983.T62500.nr20
remark:
this example took 29:33 wall clock on a single 2.67 GHz I7 core
of an 8-core system with no other significant load.
find results here:
files analogous with those in preceding examples except the OFDFT output.
additional QE Kohn-Sham output (eigenvalues and occupation
numbers for the last (or most recent) MD step) can be found here:
pwscf.save.R0.983.T62500.KPGxGxG.NBND544.ECUT75.0.ksdt.NMDSTEP5.dt80as.nr20/K00001/eigenval.xml
(after execution)
pwscf.save/K00001/eigenval.xml
(during execution)
--end--