Установка quantum espresso linux

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How to cite?

Quantum ESPRESSO is an Open Source distribution. We shall greatly appreciate if scientific work done using Quantum ESPRESSO will contain an explicit acknowledgement and the following references:

and if you used the GPU-enabled features of the code:

P. Giannozzi et al., J. Chem. Phys. 152, 154105 (2020) https://doi.org/10.1063/5.0005082

How to download?

Sources: Quantum ESPRESSO is currently distributed as source packages, but selected binary packages for Linux, Mac-OS X and Windows are also available. The current stable version (including support for NVidia GPUs) can be downloaded from:

Please read the «release-notes» file for information on major changes and problems. Patches and updates are available on GitHub: see the «Assets» list at the end of the release notes. The latest development version, in branch «develop», is available on GitLab and mirrored on GitHub.

The Schrödinger-enabled version of Quantum ESPRESSO can be downloaded here.

The RISM-enabled version of Quantum ESPRESSO can be downloaded from Satomichi Nishihara’s git repository.

Virtual Machine: A fully configured Ubuntu virtual machine that can be run from Windows/Mac-OS x/Linux/Solaris is available on the Materials Cloud site. It contains Quantum ESPRESSO and much more (4Gb).

Binaries: Binary packages for Linux are available in the Debian stable and unstable distributions, courtesy Michael Banck and DebiChem team.

Binary packages for Mac-OS X are available in the Science section of Macports.

Windows binaries are made available by AdvanceSoftware Corp.. See also the SCM site.

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1 Installation

Most installation problems have obvious origins and can be solved by reading error messages and acting accordingly. Sometimes the reason for a failure is less obvious. In such a case, you should look into Sec.2, Installation, of the user guide, and into the archive of the users’ mailing list to see if a similar problem (with solution) is described. If you get really weird error messages during installation, look for them with your preferred Internet search engine (such as Google): very often you will find an explanation and a workaround.

Also please have a look at the following page by Glenn Lockwood, containing a lot of useful info.

1.1 What Fortran compiler do I need?

Any non-buggy, or not-too-buggy, fortran-95 compiler should work, with minimal or no changes to the code. configure may not be able to recognize your system, though.

1.2 Why is configure saying that I have no fortran compiler?

Because you haven’t one (really!); or maybe you have one, but it is not in your execution path; or maybe it has been given an unusual name by your system manager. Install a compiler if you have none; if you have one, fix your execution path, or define an alias if it has a strange name. Do not pass an executable with the path as an argument to configure, as in e.g. ./configure F90=/some/strange/f95: it doesn’t work.

1.3 Why is configure saying that my fortran compiler doesn’t work?

Because it doesn’t work (really!); more exactly, configure has tried to compile a small test program and hasn’t succeeded. Your compiler may not be properly installed. For Intel compiler on PC’s: you may have forgotten to run the required initialization script for the compiler.

1.4 configure doesn’t recognize my system, what should I do?

If compilation/linking works, never mind; otherwise, try to supply a suitable supported architecture, or/and manually edit the make.sys file. Detailed instructions in Sec.2 of the user guide.

1.5 Why doesn’t configure recognize that I have a parallel machine?

You need a properly configured complete parallel environment. If any piece is missing, configure will revert to serial compilation. Detailed instructions in Sec.2 of the user guide.

1.6 Compilation fails with _internal error_, what should I do?

Any message during compilation saying something like internal compiler error and the like means that your compiler is buggy. You should report the problem to the compiler maker – especially if you paid real money for it. Sometimes reducing the optimization level, or rearranging the code in a strategic place, will make the problem disappear. In other cases you will need to move to a different compiler, or to a less buggy version (or buggy in a different way that doesn’t bug you) of the same compiler.

1.7 Compilation fails at linking stage: _symbol … not found_

If the missing symbols (i.e. routines that are called but not found) are in the code itself: most likely the fortran-to-C conventions used in file include/c_defs.h are not appropriate. Edit this file and retry.

If the missing symbols are in external libraries (BLAS, LAPACK, FFT, MPI libraries): there is a name mismatch between what the compiler expects and what the library provides. See Sec.2 of the user guide.

If the missing symbols aren’t found anywhere either in the code or in the libraries: they are system library symbols. i) If they are called by external libraries, you need to add a missing system library, or to use a different set of external libraries, compiled with the same compiler you are using. ii) If you are using no external libraries and still getting missing symbols, your compiler and compiler libraries are not correctly installed.

1.8 Compilation works but the executable doesn’t start because _shared libraries … not found_

This is a frequent problem with MKL libraries. You need to set some environment variables telling the system where the shared libraries are. See the documentation by Intel that comes with MKL libraries.

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General documentation

The general documentation (HTML or pdf ) covers the installation and usage of the current stable release of Quantum ESPRESSO (opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization). We refer the reader to the package-specific documentation for all the information on features and capabilities of Quantum-ESPRESSO.

The full Quantum ESPRESSO distribution contains the following core packages for the calculation of electronic-structure properties within Density-Functional Theory (DFT), using a Plane-Wave basis set and pseudopotentials:

• PWscf (PW) : Plane-Wave Self-Consistent Field,
• CP (CPV): Car-Parrinello Molecular Dynamics.

It also includes the following more specialized packages:

• PWneb (NEB) : energy barriers and reaction pathways through the Nudged Elastic Band method,
• PHonon : phonons with Density-Functional Perturbation Theory,
• PostProc (PP) : various utilities for data postprocessing,
• PWcond : ballistic conductance,
• GWL: GW calculations and solution of the Bethe-Salpeter Equation,
• XSPECTRA : K-edge X-ray adsorption spectra,
• TDDFPT : calculations of spectra using Time-Dependent Density-Functional Perturbation Theory,
• EPW : electron-phonon calculations using Wannier functions.

The following auxiliary codes are included as well:

• PWgui : a Graphical User Interface, producing input data files for PWscf,
• atomic : a program for atomic calculations and generation of pseudopotentials.

Several additional packages that exploit data produced by Quantum ESPRESSO or patch some Quantum ESPRESSO routines can be installed using the Makefile of Quantum ESPRESSO :

• GIPAW (Gauge-Independent Projector Augmented Waves): NMR chemical shifts and EPR g-tensor.
• WANNIER90 : maximally localized Wannier functions.
• WanT: quantum transport properties with Wannier functions.
• YAMBO: electronic excitations within Many-Body Perturbation Theory: GW and Bethe-Salpeter equation.
• PLUMED: calculation of free-energy surface through metadynamics.

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BragitOff.com

READ-LEARN-BRAG!

Downloading, Installing and an Introduction to QUANTUM ESPRESSO

Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modelling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Though it can be used on Linux, Mac and Windows, in this post I will show you how to install and use it on Linux- UBUNTU.

Downloading:

Go to this link and download the package, or download it using the terminal by giving the following command.
sudo apt-get install quantum-espresso (You can skip step 1 if you install it this way)

Installing:

Step 1:

To use Quantum Espresso, you need to extract(uncompress) the zip/tar(compressed) file that you downloaded(You don’t need to uncompress it if you used the install command).

To do that just right click on the compressed file, and select ‘Extract’.

Or you can do it using the terminal by using the following command:
tar -zxvf espresso-5.0.2.tar.gz
NOTE: Make sure you write the correct file name and version espresso-5.0.2.tar.gz . It will probably be different for you.

Once installation is done, a directory will be created with many files and other directories.

Step 2:

Now an important thing to note is that the Quantum Espresso needs a working fortran-95 compiler (most “fortran-90” compilers are ok, “g77” is not). If you don’t have it installed, the rest of the steps may not work. You can try performing the next step, if it works then you are good to go, else you need a Fortran compiler.

You can download and install a Fortran compiler by executing the following command in the terminal:

sudo apt-get install gfortran

Step 3:

Once, you have done the installation, you need to change your directory to the directory of the Quantum Espresso software, and run the following terminal command:

./configure
You can change the directory by using the command cd so if your copy of Quantum Espresso is in a directory called ‘qe-6.1’ which is in the Home directory, then you can use: cd qe-6.1

“configure” is a wrapper, calling the “install/configure” script, that tries to guess your machine and to choose compilation and linking options accordingly. “install/configure” is generated from “install/configure.ac” using the complex but well-known Unix utility “autoconf”. The result of “configure” is a file called “make.sys” containing the compilation and linking options. You may want to have a look at it to verify what “configure” thinks about your system. Several options to “configure” may (and sometimes, have to) be specified (see below).
If you get a message “architecture xxx not recognized”, specify option “ARCH=…”, such as e.g. (for a BlueGene machine):
./configure ARCH=ppc64-bg

If “configure” selects a compiler you don’t like (or one that doesn’t like Quantum ESPRESSO) specify option “F90=…” or “MPIF90=…”, e.g.:
./configure F90=gfortran

If everything is fine you should get a bunch of (mostly obscure and irrelevant) messages but no error. Read the last lines: you may need to understand them if something goes wrong at compilation stage, or if you need to boost performances.

Once this is done, you can compile the packages you will be needing. If you need to perform Plane Wave SCF calculation then you need to compile the ‘pw’ package. To do that run the following command:

make pw

“make” is another complex but standard unix utility that compiles what is needed in the way it is needed and in the order in which is needed (in Fortran-90 you need to compile modules before programs that use them, for instance). The configuration files for “make” are either coming with the package or are generated by “configure”. If everything goes well, executables will appear in “bin/”:
ls bin/*.x

You can compile all the available packages at once by running:

Step 4:

Once you’re done with the above steps, it means you now have the necessary tools to perform a pw scf calculation.
To perform such a calculation, you need an input file for Quantum Espresso. You can download the sample input file from this link. Once you have the file, save it in a directory of your choice. For the sake of this tutorial, let’s say you save it in a directory called ‘QE’ inside the Quantum Espresso installation directory.

Now, create a directory called ‘temp’ inside the directory that contains the input file(in our example the directory is ‘QE’).

Now let me tell you a little about the input file that we have here. In this file, we are basically trying to find out some of the properties for a Cu atom, like the total energy, etc.

The input file is a really important file and you will need to learn quite a few things to be able to build one yourself.
There are a lot of things that need explaining there, but I guess I will leave that for another post, and in this tutorial we will, just focus on running our first pw scf calculation. For the sake of the tutorial you can download the input file that I will be using from here or you can just copy the following and save it in a file called in .
&control
prefix=»
outdir=’temp’
pseudo_dir = ‘.’,
/
&system
ibrav= 2, celldm(1) =6.824, nat= 1, ntyp= 1,
ecutwfc =30.0,
occupations=’smearing’, smearing=’mp’, degauss=0.06
/
&electrons
/
ATOMIC_SPECIES
Cu 63.546 Cu.pbesol-dn-kjpaw_psl.0.2.UPF
ATOMIC_POSITIONS
Cu 0.00 0.00 0.00
K_POINTS automatic
8 8 8 0 0 0

Step 5:

Now the last thing you need to do is to get the pseudopotential for your atom.
If you open the input file using a text editor, you will notice the field: pseudo_dir = ‘ ‘, inside the &control section.

Inside the single quotes you need to specify the directory of your pseudopotential. But before that you first need to download one from here. Once you go to the link you can click on any atom to get a list of it’s available pseudopotentials. For this tutorial, we need a particular potential for Cu. So click on Cu(29) in the periodic table shown. Now you will see a list of a variety of potentials. Just search for this one : ‘Cu.pbesol-dn-kjpaw_psl.0.2.UPF’ and download it.

Step 6:

Once the execution is done, you will notice a file named out created in the directory with the input file.
Open and you can find information regarding the energies, how many iterations it took to converge, and more.

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