Important notice: due to the lack of time and of manpower, this manual does not cover all the topics it should, may occasionally contain outdated or incorrect information.
The intended audience of this guide is everybody who wants to:
People who want to know about the capabilities of QE, or who want just to use it, should read the User Guide instead of (or in addition to) this guide. In addition to the general User Guide, there are also package-specific guides.
People who want to know about the methods or the physics behind QE should read first the relevant literature (some pointers in the User Guide).
You can contribute to a better QE, even as an ordinary user, by:
QE is not a monolithic code, but a distribution (an integrated suite) of ``packages'', with varying degrees of integration, that can be installed on demand, or sometimes independently. The core distribution includes:
Finally there are plugins: these modify QE packages, adding new functionalities. Currently the following plugins are available:
If you want to get involved as a developer and contribute serious or nontrivial stuff (or even simple and trivial stuff), you should first of all register on GitLab.com, following the instructions (you may even use other pre-existing accounts).
All QE developers are strongly invited to subscribe to the developers' mailing list using the link in https://lists.quantum-espresso.org/mailman/listinfo/developers. Those who don't, i) miss the opportunity to follow what is going on, ii) lose the right to complain if something has gone into a direction they don't like.
Important notice: the development model of QE has undergone significant changes after release 6.2.1. The development has moved to GitLab. The official git repository is visible at git.quantum-espresso.org and can be downloaded as follows:
git clone https://gitlab.com/QEF/q-e.git
There is also a GitHub mirror github.com/QEF/q-e, only for ``pull'' (i.e., read) operations, automatically kept aligned with the official GitLab repository. The GitHub repository can be downloaded as follows: git clone https://github.com/QEF/q-e.git.
See Sect.10, ``Using git'', and file CONTRIBUTING.md, for instructions on how to use git.
It is possible to contribute:
As a rule: if you plan to make a public release of your work, you should always keep your work aligned to the current development version of QE. This is especially important if your project
The sole exception is when your changes are either relatively small, or localized to a small part of QE, or they are quite independent anyway from the rest of QE. In that case, you may just send a patch or the modified routine(s) to an expert developer who will review it and take the appropriate steps. The preferred path is however a ``merge request'' on GitLab (see Sect.10),
Important: keep your modified copy of the distribution aligned to the repository. Don't work for years, or even for months, without keeping an eye to what is going on in the repository. This is especially true for projects that modify or use QE code and routines. Update your copy frequently, verify if changes made meanwhile by other developers conflict with your changes. If your project just uses the QE installation procedure and/or data files, it is less likely to run into problems, since major incompatible changes are quite rare. You may still need to verify from time to time that everything keeps working, though.
Since Release 6.2.1, releases are distributed as ``Tags'' on GitLab. V. 6.2.1 is also the last release distributed as ``tarballs'' on qe-forge.org.
The automatic downloading of packages is implemented in file install/plugins_makefile and configured in file install/plugins_list. For independently released packages, it is sufficient to update links.
The directory structure of QE reflects its organization into packages. Each package is stored into a specific subdirectory. In addition, there is a set of directories, common to all packages, containing common code, libraries, installation utilities, general documentation.
The most important files and directories in the root (q-e/) directory are:
Makefile examples/ Doc/ src/ ...but some packages have a slightly different structure (e.g., PHonon has three directories for sources and none is called src/ ).
Let us review the files related to compilation and linking:
|-||install/: documentation and utilities for compilation and linking|
|-||configure: wrapper for install/configure script|
|-||.inc: produced by configure, contains machine-specific compilation and linking options|
|-||Makefile: contains dependencies and targets used by command make.|
|-||include/: files to be included into sources, to be pre-processed.|
make target checks for dependencies, recursively goes into subdirectories executing make again. The behavior of make is thus determined by many Makefile's in the various directories. The most important files are Makefile's in the directories containing sources, e.g. Modules/Makefile, PW/src/Makefile.
Dependencies of Fortran files are contained in make.depend files in each source directory. These files must be updated if you change the sources, running script install/makedeps.sh or using command make depend.
include make.incContains machine- and QE-specific definitions
default : @echo 'to install, type at the shell prompt:' ...If no target specified, ask for one, giving a list of possibilities
pw : pwlibs if test -d PW ; then \ ( cd PW ; $(MAKE) TLDEPS= all || exit 1) ; fiTarget pw: first check the list of dependencies (pwlib in this case), do what is needed; then go into PW/ and give command make all. Note the use of exit 1, which is required to forward the exit status of the sub-directory make to this makefile, since the section in parenthesis is run in a subshell and the if / fi block will otherwise ``hide'' its return status and ``make'' will continue in case of errors. See below for the meaning of TLDEPS.
gipaw : pwlibs ( cd install ; $(MAKE) -f plugins_makefile $@ || exit 1 )Target gipaw: do target pwlibs, then go into directory install/, execute make gipaw using plugins_makefile as Makefile. This will check if GIPAW is there, download from the network if not, compile and link it
libblas : cd install ; $(MAKE) -f extlibs_makefile $@Target libblas: this is an external library, that may or may not be needed, depending upon what is written in make.inc. If needed, go into directory install/ where make libblas using extlibs_makefile as Makefile will check if BLAS are there, download from the network if not, compile and build the library
sinclude ../make.inc default : all all: pw pwtools pw: ( cd src ; $(MAKE) all || exit 1 ) pwtools: pw ( cd tools ; $(MAKE) all || exit 1 ) ...Target pw: go into src/ if it exists, and (apart from make wizardry) give command make pw. It is important that pwtools explicitly depends upon pw or else this makefile will break when calling parallel make using make -j# Other targets are quite similar: go into a subdirectory, e.g. Doc/ and 'make something', e.g. make clean.
include ../../make.incContains machine- and QE-specific definitions
MODFLAGS= $(BASEMOD_FLAGS) \ $(MOD_FLAG)../../dft-d3/Location of needed modules, used in make.inc; BASEMOD_FLAG, MOD_FLAG are defined in make.inc
PWOBJS = \ pwscf.oObject file containing main program (this is actually redundant)
PWLIBS = \ a2fmod.o \ ... wannier_enrg.oList of objects - add here new objects, or delete from this list. Do not forget the backslash! It ensure continuation of the line
QEMODS=../../Modules/libqemod.a \ ../../KS_Solvers/libks_solvers.a \ ...F95 module objects needed for compiling and linking
TLDEPS=bindir libs mods libks_solvers dftd3TLDEPS=Top-Level DEPendencieS: a machinery to ensure proper compilation with correct dependencies also if compiling from inside a package directory and not from top level. In the top-level Makefile, TLDEPS is set to an empty string (TLDEPS=) and transmitted to Makefiles in the subdirectories. These contain a target "tldeps" that does nothing if TLDEPS is empty (i.e. executing from the top level); it goes to the top-level directory and executes TLDEPS otherwise. TLDEPS in subdirectory Makefiles must be set to the same dependencies of the intended target (e.g. pw.x in the following example) in the top-level Makefile.
all : tldeps pw.x ...Targets that will be build - add here new executables
pw.x : $(PWOBJS) libpw.a $(LIBOBJS) $(QEMODS) $(LD) $(LDFLAGS) -o $@ \ $(PWOBJS) libpw.a $(QEMODS) $(LIBOBJS) $(QELIBS) - ( cd ../../bin; ln -fs ../PW/src/$@ . ; \ ln -fs ../PW/src/$@ dist.x ; ln -fs ../PW/src/$@ manypw.x ; )Target pw.x - produces executable with the same name. It also produces a link to the executable in espresso/bin/ and two more links with different names (and different functionalities). Do not forget tabulators even if you do not see them! All variables (introduced by $) are either defined locally in Makefile or imported from make.inc
libpw.a : $(PWLIBS) $(AR) $(ARFLAGS) $@ $? $(RANLIB) $@This builds the library libpw.a - again, do not forget tabulators
tldeps: test -n "$(TLDEPS)" && ( cd ../.. ; $(MAKE) $(TLDEPS) || exit 1) || :second part of the TLDEPS machinery
clean : - /bin/rm -f *.x *.o *.a *~ *_tmp.f90 *.d *.mod *.i *.LThere should always be a ''clean'' target, removing all compiled (*.o) or preprocessed (*.F90) stuff - compiled F95 modules may have different filenames: the four last items cover most cases
include make.dependContains dependencies of objects upon other objects. Sample content of file make.depend (can be produced by install/makedep.sh):
a2fmod.o : ../../Modules/io_files.o a2fmod.o : ../../Modules/io_global.o a2fmod.o : ../../Modules/ions_base.o a2fmod.o : ../../Modules/kind.o a2fmod.o : pwcom.o a2fmod.o : start_k.o a2fmod.o : symm_base.otells us that the listed objects must have been compiled prior to compilation of a2fmod.o - make will take care of this.
BEWARE: the Makefile system is in a stable but delicate equilibrium, resulting from many years of experiments on many different machines. Handle with care: what works for you may break other cases.
BEWARE 2: parallel make (make -j N) works only if all needed dependencies are in place. Note that parallel make does not necessarily execute targets in the order they appear, e.g.: if you have
all : a b c dand "d" depends upon "a", that dependency must be explicitly present in the Makefiles, or else parallel make will not work (or will work only erratically).
Fortran source code contains preprocessing option with the same syntax used by the C preprocessor cpp. Most Fortran compilers understand preprocessing options -D ... or some similar form. Some old compilers however do not support or do not properly implement preprocessing. In this case the preprocessing is done using cpp. Normally, configure takes care of this, by selecting the appropriate rule @f90rule@ below, in this section of file make.inc.in:
.f90.o: @f90rule@and producing the appropriate file .inc.
Preprocessing is useful to
The following capabilities of the C preprocessor are used:
#if defined (__expression) ...code A... #else ...code B... #endifIf __expression is defined (with a #define command or from the command line with option -D__expression), then ...code A... is sent to output; otherwise ...code B... is sent to output.
#if defined (XXX), not
#if defined XXXor
The configure script in the root directory of QE is a wrapper that calls install/configure. This is in turn generated, using the autoconf GNU utility (http://www.gnu.org/software/autoconf/), from its source file configure.ac and the m4 files install/m4/*.m4. Don't edit install/configure directly: whenever it gets regenerated, your changes will be lost. Instead, in the install/ directory, edit configure.ac and files install/m4/*.m4, then run autoconf. If you want to keep the old configure, make a copy first.
GNU autoconf is installed by default on most Unix/Linux systems. If you don't have it on your system, you'll have to install it. You will need autoconf v.2.69 or later.
configure.ac is a regular Bourne shell script (i.e., "sh" - not csh!), except that:
|-||AC_QE_SOMETHING is a m4 macro, defined in file install/m4/x_ac_qe_something.m4. This is what you should normally modify.|
|-||all other capitalized names starting with AC_ are autoconf macros. Normally you shouldn't have to touch them.|
|-||square brackets are normally removed by the macro processor. If you need a square bracket (that should be very rare), you'll have to write two.|
You may refer to the GNU autoconf Manual for more info.
make.inc.in is the source file for .inc, that configure generates: you might want to edit that file as well. The generation procedure is as follows: if configure.ac contains the macro "AC_SUBST(name)", then every occurrence of "@name@" in the source file will be substituted with the value of the shell variable "name" at the point where AC_SUBST was called.
Similarly, configure.msg is generated from configure.msg.in: this file is only used by configure to print its final report, and isn't needed for the compilation. We did it this way so that our configure may also be used by other projects, just by replacing the QE-specific configure.msg.in by your own.
configure writes a detailed log of its operation to config.log. When any configuration step fails, you may look there for the relevant error messages. Note that it is normal for some checks to fail.
Subdirectory clib/ contains libraries written in C
(*.c). To ensure that fortran can call C routines,
use the fortran-95 intrinsic iso_c_binding module.
See Modules/wrappers.f90 for inspiration and examples.
Reference documentation can be found for instance here:
G-vectors are generated in the ggen and ggens subroutines of Modules/recvec_subs.f90. You may also have a look at routine PW/src/n_plane_waves.f90 to understand how things work. For the simple case of a single grid, G-vectors are determined by the condition
|Ec = 4Ewc||(1)|
Plane waves used in the expansion of orbitals at a specific k point are determined by the condition
In order to manage the G-vectors for each k-point, you can use the arrays ngk (number of G-vectors for each k-point) and igk_k (index of G corresponding to a given index of k + G; basically an index that allows you to identify the G-vectors corresponding to a given k and order them).
For example the kinetic energy corresponding to a given k-point ik is
g2kin(1:ngk(ik)) = ( ( xk(1,ik) + g(1,igk_k(1:ngk(ik),ik)) )**2 + & ( xk(2,ik) + g(2,igk_k(1:ngk(ik),ik)) )**2 + & ( xk(3,ik) + g(3,igk_k(1:ngk(ik),ik)) )**2 ) * tpiba2where tpiba2 = (2/a)2.
There is only one FFT for the wavefunctions so the grid does not depend upon the k-points; however, for a given wavefunction, only the components corresponding to G-vectors that satisfy (+)2/2meEwc are different from 0.
(adapted from an answer by Dario Rocca).
In calculations using only the point (k=0), the Kohn-Sham orbitals can be chosen to be real functions in real space, so that (G) = (- G). This allows us to store only half of the Fourier components. Moreover, two real FFTs can be performed as a single complex FFT. The auxiliary complex function is introduced: (r) = (r) + i(r) whose Fourier transform (G) yields
(G) = ,(G) = .
A side effect on parallelization is that G and - G must reside on the same processor. As a consequence, pairs of columns with Gn'1, n'2, n'3 and G-n'1,-n'2, n'3 (with the exception of the case n'1 = n'2 = 0), must be assigned to the same processor.
psi( 1, 1, 1) psi( 2, 1, 1) ... psi(nr1x, 1, 1) psi( 1, 2, 1) psi( 2, 2, 1) ... psi(nr1x, 2, 1) ... ... psi(nr1x,nr2x, 1) ... psi(nr1x,nr2x,nr3x) etcLet ind be the position of the (i,j,k) element in the above list: the following relation
ind = i + (j - 1) * nr1x + (k - 1) * nr2x * nr1xholds. This should clarify the relation between 1D and 3D indexing. In real space, the (i,j,k) point of the FFT grid with dimensions nr1 (nr1x), nr2 (nr2x), , nr3 (nr3x), is
The distinction between the dimensions of the FFT grid, (nr1,nr2,nr3) and the physical dimensions of the array, (nr1x,nr2x,nr3x) is done only because it is computationally convenient in some cases that the two sets are not the same. In particular, it may be convenient to have nrx1=nr1+1 to reduce memory conflicts. Note however that this possibility is not present with most common FFT's any longer, so it may be consider as obsolescent.
The two main packages, PWscf and CP, support restarting from interrupted calculations. Restarting is trivial in CP: it is sufficient to save from time to time a restart file containing wavefunctions, orthogonality matrix, forces, atomic positions, at the current and previous time step.
Restarting is much more complicated in PWscf. Since v.5.1. restarting from interrupted calculations is possible ONLY if the code has been explicitly stopped by user. It is not practical to try to restart from any possible case, such as e.g. crashes. This would imply saving lots of data all the time. With modern machines, this is not a good idea. Restart in PWscf currently works as follows:
In MPI parallelization, a number of independent processes are started on as many processors, communicating via calls to MPI libraries (the code will work even with more than one process per processor, but this is not a smart thing to do). Each process has its own set of variables and knows nothing about other processes' variables. Variables that take little memory are replicated on all processors, those that take a lot of memory (wavefunctions, G-vectors, R-space grid) are distributed.
Calls to MPI libraries should be confined to a few selected places, not scattered everywhere into the source code. The vast majority of parallel operations consist either in broadcasts from one processor to all others, or in global operations: parallel sums and transpose. All you need is the MPI communicator (plus the ID of the root processor for broadcasts), and the appropriate call to wrapper routines, contained in UtilXlib/mp.f90 and UtilXlib/mp_base.f90. For instance: mp_sum is a wrapper to mpi_reduce, mp_bcast to mpi_bcast.
For efficiency reasons (latency is very significant), performing many parallel operations on a small amount of data each must be avoided. If you can, store a sizable amount of data and transmit it in a single MPI call. An example of REALLY BAD code:
COMPLEX, ALLOCATABLE :: wfc(:,:), swfc(:,:) ALLOCATE (wfc(npwx,m),swfc(npwx,m)) DO i=1,m DO j=1,m ps = zdotc(npw,wfc(1,i),1,swfc(1,j)1) CALL mp_sum(ps,intra_bgrp_group) END DO END DOMUCH better code, both for serial and parallel speed:
COMPLEX, ALLOCATABLE :: ps(:,:), wfc(:,:), swfc(:,:) ALLOCATE (ps(m,m), wfc(npwx,m),swfc(npwx,m)) CALL zgemm ('c', 'n', m, m, npw, (1.d0, 0.d0), wfc, & npwx, swfc, npwx, (0.d0, 0.d0), ps, m) CALL mp_sum(ps,intra_bgrp_group)
Calls to MPI libraries require variables contained into a mpif.h file, or in a mpi module in more recent implementations, that is usually absent on serial machines. In order to prevent compilation problems on serial machines, the following rules must be followed:
\#if defined (__MPI)}to prevent compilation and usage in the serial case. Note that some compilers do not like empty files or modules containing nothing!
\#if defined (__MPI)}are needed only when the flux of parallel and serial execution differ.
__PARAmust not be used.
mp_world.f90 is the module containing all processors on which QE is running. world_comm is the communicator between all such processors. In QE, its usage should be confined to parallel environment initialization. It should not be used in source code, unless this is used only by stand-alone executables that perform simple auxiliary tasks and do not allow for multiple parallelization levels. Unless QE is started from an external code, world_comm will in practice coincides with MPI_WORLD_COMM.
mp_image.f90 is the module containing information about ``image" parallelization, i.e. division into quasi-independent similar calculations, each taking care of a different set of atomic positions (NEB, PWscf) or of different irreps/phonon wavevectors (PHonon). intra_image_comm is the communicator between processors of the same image (most of the action will happen here); inter_image_comm is the communicator between processors belonging to different images (should be used only when communication between images is necessary). intra_image_comm and world_comm coincide if there is just one image running.
mp_pools.f90 is the module containing information about k-point (``pool") parallelization. intra_pool_comm is the communicator between processors working on the same group (``pool") of k-points; inter_pool_comm is the communicator between different k-point pools. Note that:
intra_pool_comm and intra_image_comm coincide if there is just one k-point pool.
mp_bands.f90 is the module containing information about band parallelization. intra_bgrp_comm is the communicator between processors of the same group of bands; inter_band_comm is the communicator between processors belonging to different groups of bands. Note that band parallelization is currently implemented only in CP and for hybrid functionals in PW. When a sum over all bands is needed:
intra_bgrp_comm and intra_pool_comm coincide if there is just one band group.
Plane waves ( + or vectors up to the specified kinetic energy cutoff) are distributed across processors of the intra_bgrp_comm communicators. Sums over all plane waves or G-vectors (as e.g. in scalar products |) should be performed as follows:
The same holds for real-space FFT's grid.
IF ( ionode ) THEN OPEN ( ..., IOSTAT=ierr ) ... END IF CALL mp_bcast( ierr, ... , intra_image_comm ) CALL errore( 'routine','error', ierr )The same applies to all operations performed on a single processor, or a subgroup of processors: any error code must be broadcast before the check.
Quantum ESPRESSO employ arrays whose memory requirements fall into three categories.
Requirements: the data file should be
There are currently no strict guidelines for developers. You should however follow at least the following loose ones:
#if defined (XXX), not
#if defined XXXor
INTEGER, INTENT(IN) :: N REAL(dp), INTENT(OUT) :: A(N)in this order (some compilers complain if you put the second line before the first).
New input variables should be added to ''Modules/input_parameters.f90'', then copied to the code internal variables in the ''input.f90'' subroutine. The namelists and cards parsers are in ''Modules/read_namelists.f90'' and ''Modules/read_cards.f90''. Files ''input_parameters.f90'', ''read_namelists.f90'', ''read_cards.f90'' are shared by all codes, while each code has its own version of ''input.f90'' used to copy input values into internal variables
EXAMPLE: suppose you need to add a new input variable called ''pippo'' to the namelist control, then:
INTEGER :: pippo = 0 NAMELIST / control / ....., pippoRemember: always set an initial value!
subroutine control_default( prog ) ... IF( prog == 'PW' ) pippo = 10 ... end subroutineThis routine sets the default value for pippo (can be different in different codes)
subroutine control_bcast( ) ... call mp_bcast( pippo, intra_image_comm ) ... end subroutine
The documentation must be processed with command ``make doc'' before the release. Note that:
The following notes cover the QE-specific work organization, plus the
essential git commands. Those interested in mastering git may consult
one of the many available on-line guides and tutorials, e.g.,
The git repository is hosted on GitLab:
A mirror, automatically aligned every week, is available
https://github.com/QEF/q-e. To download the repository:
Registration on GitLab is not needed at this stage but it is useful anyway. GitLab accepts a number of other accounts (Google, GitHub, ...) to sign in.
git clone https://gitlab.com/QEF/q-e.gitor
git clone email@example.com:QEF/q-e.git
The repository contains a ``master'' and a ``develop'' branch, plus other branches for specific goals. The ``develop'' branch is the default and is where development goes on. The ``master'' branch is aligned to the ``develop'' branch from time to time, when ``develop'' looks stable enough. No other changes are allowed in ``master'' except for serious bugs.
Development can proceed in different ways:
https://gitlab.com/QEF/q-e, use the ``fork'' button
git clone firstname.lastname@example.org:<your-username>/q-e.git
git checkout --track origin/develop
then create a new branch and work on it:
git pull email@example.com:QEF/q-e.git develop
(if the branch exists, use
git checkout -bmy-new-branch
git checkoutmy-branch to switch to it. If your local repository contains unsaved changes, commit or "stash" them before switching branch).
Once you have made your changes, commit (save) then:
Please when committing BE EXTREMELY CAREFUL not to add files that do not belong to the repository, e.g.: data files, executables, objects. These files MUST NOT BE COMMITTED. Once you are finished with changes, you have to push (publish) to the remote repository:
git addlist-of-changed-or-added-files , then
git commit, or
git commitlist-of-changed-files, or
git commit -a(commits all modified files)
git push originmy-new-branch
git pushif the remote branch my-new-branch already exists. The reply message should contain a link that allows you to make a ``merge request'' (the link works only if you are signed in to gitlab.com). You can also use the GitLab web interface to that end. The branch may be automatically removed after the merge (set the appropriate option if you approve your merge) or using
git branch -dmy-new-branch.
Note: if a merge request is pending and you push further changes to the branch to be merged, the merge request will be automatically updated. If this is not what you want, commit to a different branch, or wait until the merge is done.
It may be a good idea to align your branch to the current development version before the merge request. If you have modified a file that has meanwhile been modified in the repository, a conflict will arise. You can use git stash to resolve the conflict:
Beware! you may need to manually merge files that have been modified both by you and in the repository. git stash -l list all stashed changes in reverse chronological order. The stash can be cleared using git stash clear.
git stash save(save and remove modified files)
git pull ...(update files)
git stash apply(overwrite with locally modified files)
Note: if you do not change sources but only documentation, tests, examples,
[skip ci] in the commit message. This prevents execution of
automatic compilation on GitLab (that sometimes fails for no good reason,
blocking a subsequent merge request).
Note: a commit message containing
[fixes issue #N] should
automatically mark issue N to as solved once it is merged.
git clone firstname.lastname@example.org:QEF/q-e.gitif not already done
git checkout --track origin/develop
The QE test-suite is used to ensure continuous integration and long-term numerical stability of the code. The test-suite is also used by different Buildbot test-farm to automatically test the code nightly after a commit to the repository has been detected.
The currently active test-farm machine can be accessed at
test-farm.quantum-espresso.org (points to a machine at CINECA:
Let us take the example of adding a new test for the TDDFPT module.
[tddfpt_*/] program = TDDFPTThis means that all the new tests related to TDDFPT must be placed in a folder with a name that starts with tddfpt_. You can also add it to a new category.
make run-custom-test testdir=tddfpt_CH4We can then rename the output by doing
cp test.out.030117.inp=CH4.pw-in.args=1 benchmark.out.git.inp=CH4.pw-in.args=1We now have a reference file for the first step of the calculation. We can do the same for the two other steps.
Once this is done. We can clean all the unwanted files and we should be left with a clean folder that can be committed to the svn repo. In our case the test folder contains the following files:
benchmark.out.git.inp=CH4.pw-in.args=1 benchmark.out.git.inp=CH4.tddfpt_pp-in.args=3 benchmark.out.git.inp=CH4.tddfpt-in.args=2 CH4.tddfpt-in CH4.pw-in CH4.tddfpt_pp-in
It is very important to then re-run the tests in parallel (4 cores) to be sure that the results are within the accepted tolerance.
You have to create a new folder following the convention prog_name and test_name and then follow the structure outline above. If you want to test new physical quantities, you need to parse them using the script extract-PROG_NAME.x. Finally, the new test should be added in jobconfig.
In order to support a previously unsupported architecture, first you have to figure out which compilers, compilation flags, libraries etc. should be used on that architecture. In other words, you have to write a .inc that works: you may use the manual configuration procedure for that (see the User Guide). Then, you have to modify configure so that it can generate that .inc automatically.
To do that, you have to add the case for your architecture in several places throughout configure.ac:
Look for these lines:
if test "$arch" = "" then case $host in ia64-*-linux-gnu ) arch=ia64 ;; x86_64-*-linux-gnu ) arch=x86_64 ;; *-pc-linux-gnu ) arch=ia32 ;; etc.Here you must add an entry corresponding to your architecture and operating system. Run config.guess to obtain the string identifying your system. For instance on a PC it may be "i686-pc-linux-gnu", while on IBM SP4 "powerpc-ibm-aix18.104.22.168". It is convenient to put some asterisks to account for small variations of the string for different machines of the same family. For instance, it could be "aix4.3" instead of "aix5.1", or "athlon" instead of "i686"...
Look for these lines:
# candidate compilers and flags based on architecture case $arch in ia64 | x86_64 ) ... ia32 ) ... aix ) ... etc.
Add an entry for your value of $arch, and set there the appropriate values for several variables, if needed (all variables are assigned some reasonable default value, defined before the "case" block):
- "try_f90" should contain the list of candidate Fortran 90 compilers, in order of decreasing preference (i.e. configure will use the first it finds). If your system has parallel compilers, you should list them in "try_mpif90".
- "try_ar", "try_arflags": for these, the values "ar" and "ruv" should be always fine, unless some special flag is required (e.g., -X64 With sp4).
- you should define "try_dflags" if there is any preprocessing option specific to your machine: for instance, on IBM machines, "try_dflags=-D__AIX" . A list of such flags can be found in file include/defs.h.README.
You shouldn't need to define the following: - "try_iflags" should be set to the appropriate "-I" option(s) needed by the preprocessor or by the compiler to locate *.h files to be included; try_iflags="-I../include" should be good for most cases
For example, here's the entry for IBM machines running AIX:
aix ) try_mpif90="mpxlf90_r mpxlf90" try_f90="xlf90_r xlf90 $try_f90" try_arflags="-X64 ruv" try_arflags_dynamic="-X64 ruv" try_dflags="-D__AIX -D__XLF" ;;The following step is to look for both serial and parallel fortran compilers:
# check serial Fortran 90 compiler... ... AC_PROG_F77($f90) ... # check parallel Fortran 90 compiler ... AC_PROG_F77($mpif90) ... echo setting F90... $f90 echo setting MPIF90... $mpif90A few compilers require some extra work here: for instance, if the Intel Fortran compiler was selected, you need to know which version because different versions need different flags.
At the end of the test,
- $mpif90 is the parallel compiler, if any; if no parallel compiler is found or if -disable-parallel was specified, $mpif90 is the serial compiler
- $f90 is the serial compiler
Next step: the choice of (serial) C and Fortran 77 compilers. Look for these lines:
# candidate C and f77 compilers good for all cases try_cc="cc gcc" try_f77="$f90" case "$arch:$f90" in *:f90 ) .... etc.Here you have to add an entry for your architecture, and since the correct choice of C and f77 compilers may depend on the fortran-90 compiler, you may need to specify the f90 compiler as well. Again, specify the compilers in try_cc and try_f77 in order of decreasing preference. At the end of the test,
- $cc is the C compiler
- $f77 is the Fortran 77 compiler, used to compile *.f files (may coincide with $f90)
Look for these lines:
# check Fortran compiler flags ... case "$arch:$f90" in ia64:ifort* | x86_64:ifort* ) ... ia64:ifc* ) ... etc.Add an entry for your case and define:
- "try_fflags": flags for Fortran 77 compiler.
- "try_f90flags": flags for Fortran 90 compiler. In most cases they will be the same as in Fortran 77 plus some others. In that case, define them as "$(FFLAGS) -something_else".
- "try_fflags_noopt": flags for Fortran 77 with all optimizations turned off: this is usually "-O0". These flags used to be needed to compile LAPACK dlamch.f; likely obsolete
- "try_ldflags": flags for the linking phase (not including the list of libraries: this is decided later).
- "try_ldflags_static": additional flags to select static compilation (i.e., don't use shared libraries).
- "try_dflags": must be defined if there is in the code any preprocessing option specific to your compiler (for instance, -D__INTEL for Intel compilers). Define it as "$try_dflags -D..." so that pre-existing flags, if any, are preserved.
- if the Fortran compiler is not able to invoke the C preprocessor automatically before compiling, set "have_cpp=0" (the opposite case is the default). The appropriate compilation rules will be generated accordingly. If the compiler requires that any flags be specified in order to invoke the preprocessor (for example, "-fpp " - note the space), specify them in "pre_fdflags".
For example, here's the entry for ifort on Linux PC:
ia32:ifort* ) try_fflags="-O2 -tpp6 -assume byterecl" try_f90flags="\$(FFLAGS) -nomodule" try_fflags_noopt="-O0 -assume byterecl" try_ldflags="" try_ldflags_static="-static" try_dflags="$try_dflags -D__INTEL" pre_fdflags="-fpp " ;;Next step: flags for the C compiler. Look for these lines:
case "$arch:$cc" in *:icc ) ... *:pgcc ) ... etc.Add an entry for your case and define:
- "try_cflags": flags for C compiler.
- "c_ldflags": flags for linking, when using the C compiler as linker. This is needed to check for libraries written in C, such as FFTW.
- if you need a different preprocessor from the standard one ($CC -E), define it in "try_cpp".
For example for XLC on AIX:
aix:mpcc* | aix:xlc* | aix:cc ) try_cflags="-q64 -O2" c_ldflags="-q64" ;;Finally, if you have to use a nonstandard preprocessor, look for these lines:
echo $ECHO_N "setting CPPFLAGS... $ECHO_C" case $cpp in cpp) try_cppflags="-P -traditional" ;; fpp) try_cppflags="-P" ;; ...and set "try_cppflags" as appropriate.
To instruct configure to search for libraries, you must tell it two things: the names of libraries it should search for, and where it should search.
The following libraries are searched for:
- BLAS or equivalent. Some vendor replacements for BLAS that are supported by QE are:
MKL on Linux, 32- and 64-bit Intel CPUsMoreover, ATLAS is used over BLAS if available.
ACML on Linux, 64-bit AMD CPUs
ESSL on AIX
SCSL on sgi altix
SUNperf on sparc
- LAPACK or equivalent. Some vendor replacements for LAPACK are supported by QE, e.g.: Intel MKL, IBM ESSL
- FFTW (version 3) or another supported FFT library (e.g Intel DFTI, IBM ESSL)
- the IBM MASS vector math library
- an MPI library. This is often automatically linked by the compiler
If you have another replacement for the above libraries, you'll have to insert a new entry in the appropriate place.
This is unfortunately a little bit too complex to explain.
"AC_SEARCH_LIBS(function, name, ...)" looks for symbol "function" in library "libname.a". If that is found, "-lname" is appended to the LIBS environment variable (initially empty). The real thing is more complicated than just that because the "-Ldirectory" option must be added to search in a nonstandard directory, and because a given library may require other libraries as prerequisites (for example, Lapack requires BLAS).
Written by Paolo Giannozzi 2005-11-11, Last modified by Andrea Ferretti 2006-10-29
Format name: QEXML
Format version: 1.4.0
The "restart file" is actually a "restart directory", containing several files and sub-directories. For CP/FPMD, the restart directory is created as "$prefix_$ndw/", where $prefix is the value of the variable "prefix". $ndw the value of variable ndw, both read in input; it is read from "$prefix_$ndr/", where $ndr the value of variable ndr, read from input. For PWscf, both input and output directories are called "$prefix.save/".
The content of the restart directory is as follows:
data-file.xml which contains: - general information that doesn't require large data set: atomic structure, lattice, k-points, symmetries, parameters of the run, ... - pointers to other files or directories containing bulkier data: grids, wavefunctions, charge density, potentials, ... charge_density.dat contains the charge density spin_polarization.dat contains the spin polarization (rhoup-rhodw) (LSDA case) magnetization.x.dat magnetization.y.dat contain the spin polarization along x,y,z magnetization.z.dat (noncollinear calculations) lambda.dat contains occupations (Car-Parrinello dynamics only) mat_z.1 contains occupations (ensemble-dynamics only) <pseudopotentials> A copy of all pseudopotential files given in input <k-point dirs> Subdirectories K00001/, K00002/, etc, one per k-point.Each k-point directory contains:
evc.dat wavefunctions for spin-unpolarized calculations, OR evc1.dat evc2.dat spin-up and spin-down wavefunctions, respectively, for spin polarized (LSDA) calculations; gkvectors.dat the details of specific k+G grid; eigenval.xml eigenvalues for the corresponding k-point for spin-unpolarized calculations, OR eigenval1.xml spin-up and spin-down eigenvalues, eigenval2.xml for spin-polarized calculations;in a molecular dynamics run, also wavefunctions at the preceding time step:
evcm.dat for spin-unpolarized calculations OR evcm1.dat evcm2.dat for spin polarized calculations;
XML Header: whatever is needed to have a well-formed XML file Body: introduced by <Root>, terminated by </Root>. Contains first-level tags only. These contain only other tags, not values. XML syntax applies. First-level tags: contain either second-level tags, OR data tags: tags containing data (values for a given variable), OR file tags: tags pointing to a filedata tags syntax ( [...] = optional ) :
<TAG type="vartype" size="n" [UNIT="units"] [LEN="k"]> values (in appropriate units) for variable corresponding to TAG: n elements of type vartype (if character, of length k) </TAG>where TAG describes the variable into which data must be read;
Short syntax, used only in a few cases:
<TAG attribute="something"/> .For instance:
<FFT_GRID nr1="NR1" nr2="NR2" nr3="NR3"/>defines the value of the FFT grid parameters nr1, nr2, nr3 for the charge density
<?xml version="1.0"?> <?iotk version="1.0.0test"?> <?iotk file_version="1.0"?> <?iotk binary="F"?>These are meant to be used only by iotk (actually they aren't)
- <HEADER> (global information about fmt version) - <CONTROL> (miscellanea of internal information) - <STATUS> (information about the status of the CP simulation) - <CELL> (lattice vector, unit cell, etc) - <IONS> (type and positions of atoms in the unit cell etc) - <SYMMETRIES> (symmetry operations) - <ELECTRIC_FIELD> (details for an eventual applied electric field) - <PLANE_WAVES> (basis set, cutoffs etc) - <SPIN> (info on spin polarizaztion) - <MAGNETIZATION_INIT> (info about starting or constrained magnetization) - <EXCHANGE_CORRELATION> - <OCCUPATIONS> (occupancy of the states) - <BRILLOUIN_ZONE> (k-points etc) - <PARALLELISM> (specialized info for parallel runs) - <CHARGE-DENSITY> - <TIMESTEPS> (positions, velocities, nose' thermostats) - <BAND_STRUCTURE_INFO> (dimensions and basic data about band structure) - <EIGENVALUES> (eigenvalues and related data) - <EIGENVECTORS> (eigenvectors and related data) * Tag description <HEADER> <FORMAT> (name and version of the format) <CREATOR> (name and version of the code generating the file) </HEADER> <CONTROL> <PP_CHECK_FLAG> (whether file is complete and suitable for post-processing) <LKPOINT_DIR> (whether kpt-data are written in sub-directories) <Q_REAL_SPACE> (whether augmentation terms are used in real space) <BETA_REAL_SPACE> (whether projectors are used in real space, not implemented) </CONTROL> <STATUS> (optional, written only by CP) <STEP> (number $n of steps performed, i.e. we are at step $n) <TIME> (total simulation time) <TITLE> (a job descriptor) <ekin> (kinetic energy) <eht> (hartree energy) <esr> (Ewald term, real-space contribution) <eself> (self-interaction of the Gaussians) <epseu> (pseudopotential energy, local) <enl> (pseudopotential energy, nonlocal) <exc> (exchange-correlation energy) <vave> (average of the potential) <enthal> (enthalpy: E+PV) </STATUS> <CELL> <NON-PERIODIC_CELL_CORRECTION> <BRAVAIS_LATTICE> <LATTICE_PARAMETER> <CELL_DIMENSIONS> (cell parameters) <DIRECT_LATTICE_VECTORS> <UNITS_FOR_DIRECT_LATTICE_VECTORS> <a1> <a2> <a3> <RECIPROCAL_LATTICE_VECTORS> <UNITS_FOR_RECIPROCAL_LATTICE_VECTORS> <b1> <b2> <b3> </CELL> <MOVING_CELL> (optional, PW only) <CELL_FACTOR> <IONS> <NUMBER_OF_ATOMS> <NUMBER_OF_SPECIES> <UNITS_FOR_ATOMIC_MASSES> For each $n-th species $X: <SPECIE.$n> <ATOM_TYPE> <MASS> <PSEUDO> </SPECIE.$n> <PSEUDO_DIR> <UNITS_FOR_ATOMIC_POSITIONS> For each atom $n of species $X: <ATOM.$n SPECIES="$X" INDEX=nt tau=(x,y,z) if_pos=...> </IONS> <SYMMETRIES> (optional, PW only) <NUMBER_OF_SYMMETRIES> <NUMBER_OF_BRAVAIS_SYMMETRIES> <INVERSION_SYMMETRY> <DO_NOT_USE_TIME_REVERSAL> <TIME_REVERSAL_FLAG> <NO_TIME_REV_OPERATIONS> <NUMBER_OF_ATOMS> <UNITS_FOR_SYMMETRIES> For each symmetry $n: <SYMM.$n> <INFO> <ROTATION> <FRACTIONAL_TRANSLATION> <EQUIVALENT_IONS> </SYMM.$n> For the remaining bravais symmetries: <SYMM.$n> <INFO> <ROTATION> </SYMM.n> </SYMMETRIES> <ELECTRIC_FIELD> (optional, sawtooth field in PW only)) <HAS_ELECTRIC_FIELD> <HAS_DIPOLE_CORRECTION> <FIELD_DIRECTION> <MAXIMUM_POSITION> <INVERSE_REGION> <FIELD_AMPLITUDE> </ELECTRIC_FIELD> <PLANE_WAVES> <UNITS_FOR_CUTOFF> <WFC_CUTOFF> <RHO_CUTOFF> <MAX_NUMBER_OF_GK-VECTORS> <GAMMA_ONLY> <FFT_GRID> <GVECT_NUMBER> <SMOOTH_FFT_GRID> <SMOOTH_GVECT_NUMBER> <G-VECTORS_FILE> link to file "gvectors.dat" <SMALLBOX_FFT_GRID> </PLANE_WAVES> <SPIN> <LSDA> <NON-COLINEAR_CALCULATION> <SPIN-ORBIT_CALCULATION> <SPINOR_DIM> <SPIN-ORBIT_DOMAG> </SPIN> <MAGNETIZATION_INIT> <CONSTRAINT_MAG> <NUMBER_OF_SPECIES> For each species X: <SPECIE.$n> <STARTING_MAGNETIZATION> <ANGLE1> <ANGLE2> <CONSTRAINT_1,2,3> </SPECIE.$n> <FIXED_MAGNETIZATION_1,2,3> <MAGNETIC_FIELD_1,2,3> <TWO_FERMI_ENERGIES> <UNITS_FOR_ENERGIES> <FIXED_MAGNETIZATION> <ELECTRONS_UP> <ELECTRONS_DOWN> <FERMI_ENERGY_UP> <FERMI_ENERGY_DOWN> <LAMBDA> </MAGNETIZATION_INIT> <EXCHANGE_CORRELATION> <DFT> <LDA_PLUS_U_CALCULATION> if LDA_PLUS_U_CALCULATION <NUMBER_OF_SPECIES> <HUBBARD_LMAX> <HUBBARD_L> <HUBBARD_U> <LDA_PLUS_U_KIND> <U_PROJECTION_TYPE> <HUBBARD_J> <HUBBARD_J0> <HUBBARD_ALPHA> <HUBBARD_BETA> endif if <DFT_D2> <SCALING_FACTOR> <CUTOFF_RADIUS> <C6> <RADIUS_VDW> if <XDM> if <TKATCHENKO-SCHEFFLER> <ISOLATED_SYSTEM> </EXCHANGE_CORRELATION> if hybrid functional <EXACT_EXCHANGE> <x_gamma_extrapolation> <nqx1> <nqx2> <nqx3> <exxdiv_treatment> <yukawa> <ecutvcut> <exx_fraction> <screening_parameter> </EXACT_EXCHANGE> endif <OCCUPATIONS> <SMEARING_METHOD> if gaussian smearing <SMEARING_TYPE> <SMEARING_PARAMETER> endif <TETRAHEDRON_METHOD> if use tetrahedra <NUMBER_OF_TETRAHEDRA> for each tetrahedron $t <TETRAHEDRON.$t> endif <FIXED_OCCUPATIONS> if using fixed occupations <INFO> <INPUT_OCC_UP> if lsda <INPUT_OCC_DOWN> endif endif </OCCUPATIONS> <BRILLOUIN_ZONE> <NUMBER_OF_K-POINTS> <UNITS_FOR_K-POINTS> <MONKHORST_PACK_GRID> <MONKHORST_PACK_OFFSET> For each k-point $n: <K-POINT.$n> <STARTING_F_POINTS> For each starting k-point $n: <K-POINT_START.$n> kx, ky, kz, wk <NORM-OF-Q> </BRILLOUIN_ZONE> <PARALLELISM> <GRANULARITY_OF_K-POINTS_DISTRIBUTION> <NUMBER_OF_PROCESSORS> <NUMBER_OF_PROCESSORS_PER_POOL> <NUMBER_OF_PROCESSORS_PER_IMAGE> <NUMBER_OF_PROCESSORS_PER_TASKGROUP> <NUMBER_OF_PROCESSORS_PER_POT> <NUMBER_OF_PROCESSORS_PER_BAND_GROUP> <NUMBER_OF_PROCESSORS_PER_DIAGONALIZATION> </PARALLELISM> <CHARGE-DENSITY> link to file "charge_density.rho" </CHARGE-DENSITY> <TIMESTEPS> (optional) For each time step $n=0,M <STEP$n> <ACCUMULATORS> <IONS_POSITIONS> <stau> <svel> <taui> <cdmi> <force> <IONS_NOSE> <nhpcl> <nhpdim> <xnhp> <vnhp> <ekincm> <ELECTRONS_NOSE> <xnhe> <vnhe> <CELL_PARAMETERS> <ht> <htve> <gvel> <CELL_NOSE> <xnhh> <vnhh> </CELL_NOSE> </TIMESTEPS> <BAND_STRUCTURE_INFO> <NUMBER_OF_BANDS> <NUMBER_OF_K-POINTS> <NUMBER_OF_SPIN_COMPONENTS> <NON-COLINEAR_CALCULATION> <NUMBER_OF_ATOMIC_WFC> <NUMBER_OF_ELECTRONS> <UNITS_FOR_K-POINTS> <UNITS_FOR_ENERGIES> <FERMI_ENERGY> </BAND_STRUCTURE_INFO> <EIGENVALUES> For all kpoint $n: <K-POINT.$n> <K-POINT_COORDS> <WEIGHT> <DATAFILE> link to file "./K$n/eigenval.xml" </K-POINT.$n> </EIGENVALUES> <EIGENVECTORS> <MAX_NUMBER_OF_GK-VECTORS> For all kpoint $n: <K-POINT.$n> <NUMBER_OF_GK-VECTORS> <GK-VECTORS> link to file "./K$n/gkvectors.dat" for all spin $s <WFC.$s> link to file "./K$n/evc.dat" <WFCM.$s> link to file "./K$n/evcm.dat" (optional) containing wavefunctions at preceding step </K-POINT.n> </EIGENVECTORS>
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