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McStasMcXtrace / iFit

a simple library to analyze data (with McCode and Phonons/DFT hooks). :warning: this project has been moved to https://gitlab.com/soleil-data-treatment/soleil-software-projects/remote-desktop
http://ifit.mccode.org
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Models: Sqw: phonons: support CP2K #120

Closed farhi closed 5 years ago

farhi commented 6 years ago

ASE/CP2K requires 'cp2k_shell' to be found in the CP2K.command see https://wiki.fysik.dtu.dk/ase/ase/calculators/cp2k.html

The cp2k_shell is not part of the Debian packages. Must compile CP2K and create Debian package if this is a route to follow.

CP2K 2.6.2 Ubuntu 16.04 (from repo) does not seem to be functional with ASE as is. The '* READY' message is not detected and raises a stop.

farhi commented 6 years ago

CP2K example with ASE

which is:

$ export ASE_CP2K_COMMAND="mpirun -n 2 cp2k_shell.popt"
$ python
>>> from ase.calculators.cp2k import CP2K
>>> from ase.build import molecule
>>> calc = CP2K()
>>> atoms = molecule('H2O', calculator=calc)
>>> atoms.center(vacuum=2.0)
>>> print(atoms.get_potential_energy())
-467.191035845

But fails with:

>>> calc = CP2K()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/ase/calculators/cp2k.py", line 170, in __init__
    self._shell = Cp2kShell(self.command, self._debug)
  File "/usr/local/lib/python2.7/dist-packages/ase/calculators/cp2k.py", line 436, in __init__
    assert self.recv() == '* READY'
AssertionError

Requires fixing as MR, to be more relaxed when getting the CP2K version.

Can also look at:

farhi commented 6 years ago

The CP2K works mostly, when "get version" is not blocking, but the pseudo basis seems to be updated:

the example ends with CP2K error:

 *********************************************************************
 *** ERROR in read_gth_potential (MODULE external_potential_types) ***
 *********************************************************************

 *** The requested atomic potential <GTH-LDA> for element <H> was not ***
 *** found in the potential file <POTENTIAL>                          ***
farhi commented 6 years ago

CP2K is now version 4.1. Ubuntu 16.04 provides 2.6 (from 2015). ASE requires version 3 or newer. CP2K 4 easy to install. Has a dependency solver (install in tools/toolchain).

Could make a Debian package ??

farhi commented 6 years ago

Pushed ASE MR https://gitlab.com/ase/ase/merge_requests/601 to update CP2K calculator and use version 2.6.

To use in iFit, remains, as specified in https://wiki.fysik.dtu.dk/ase/ase/calculators/cp2k.html:

farhi commented 6 years ago

MR was refused. Go towards a CP2K build version 4.1 for Ubuntu 14.04 and 16.04.

CP2K 4.1 compile:

farhi commented 6 years ago

CP2K version 4.1 compiles with OpenMPI, ScaLAPACK and BLACS, after installing the toolchain.Then the 'arch' file for the makefile dependencies is "local.popt":

CC          = gcc
CXX         = g++
CPP         =
AR          = ar -r
FC          = mpif90
LD          = mpif90
#
DFLAGS      = -D__LIBXSMM  -D__parallel -D__MPI_VERSION=2 -D__FFTW3  -D__LIBINT -D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5 -D__LIBXC -D__SCALAPACK
#
WFLAGS      = -Werror=aliasing -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs -Werror=realloc-lhs-all -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable -Werror=unused-dummy-argument -Werror=conversion -Werror=uninitialized -Wno-maybe-uninitialized  
#
FCDEBFLAGS  = -ffree-form -std=f2003 -fimplicit-none 
CFLAGS      = -march=native -fno-omit-frame-pointer -g  -O3 -funroll-loops -ffast-math $(PROFOPT)    -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/fftw-3.3.4/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libint-1.1.4/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxc-2.2.2/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxsmm-1.4.4/include' $(DFLAGS)
FCFLAGS     = -march=native -fno-omit-frame-pointer -g  -O3 -funroll-loops -ffast-math $(PROFOPT)    -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/fftw-3.3.4/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libint-1.1.4/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxc-2.2.2/include' -I'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxsmm-1.4.4/include' $(FCDEBFLAGS) $(WFLAGS) $(DFLAGS)
#
LDFLAGS     = $(FCFLAGS) -Wl,--enable-new-dtags    -L'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/fftw-3.3.4/lib' -Wl,-rpath='/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/fftw-3.3.4/lib' -L'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libint-1.1.4/lib' -Wl,-rpath='/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libint-1.1.4/lib' -L'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxc-2.2.2/lib' -Wl,-rpath='/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxc-2.2.2/lib' -L'/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxsmm-1.4.4/lib' -Wl,-rpath='/home/farhi/Downloads/cp2k-4.1/tools/toolchain/install/libxsmm-1.4.4/lib' 
LIBS        =  -lxsmmf -lxsmm -lxcf90 -lxc -lderiv -lint -lfftw3 -lstdc++  -lscalapack-openmpi -lblacs-openmpi -lblacsCinit-openmpi -lblas -llapack

making cp2k-4.1-trusty package...

farhi commented 6 years ago

Done. Debian packages available at http://packages.mccode.org/

farhi commented 6 years ago

KPoints keyword is missing in ASE/Calculators/cp2k

According to

the syntax should be something like:

&FORCE_EVAL
    &DFT
        &KPOINTS
            SCHEME MONKHORST-PACK 3 3 1
            FULL_GRID .TRUE.        
               &END KPOINTS
    &END DFT
&END FORCE_EVAL
farhi commented 6 years ago

Not in ASE/CP2k either: smearing nbands etol that's bad.

farhi commented 6 years ago

Ole Schütt pushed a kpoints support for CP2K in his own branch of ASE:

see https://gitlab.com/oschuett/ase/commit/933b9863670f0bcc0673c1243fc53495d34c62b3

There is as well a test with Si. Should try.