[Wien] Problem when running MPI-parallel version of LAPW0
Dear Pr. Blaha, Dear Wien2k users, We tried to install the last version of Wien2k (14.1) on a supercomputer and we are facing some troubles with the MPI parallel version. 1)lapw0 is running correctly in sequential, but crashes systematically when the parallel option is activated (independently of the number of cores we use): lapw0 -p(16:08:13) starting parallel lapw0 at lun. sept. 29 16:08:13 CEST 2014 .machine0 : 4 processors Child id1 SIGSEGV Child id2 SIGSEGV Child id3 SIGSEGV Child id0 SIGSEGV **lapw0 crashed! 0.029u 0.036s 0:50.91 0.0%0+0k 5248+104io 17pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed stop error w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault Child with myid of1has an error 'Unknown' - SIGSEGV Child id1 SIGSEGV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 **lapw0 crashed! cat: No match.0.027u 0.034s 1:33.13 0.0%0+0k 5200+96io 16pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed 2) lapw2 also crashes sometimes when MPI parallelization is used. Sequential or k-parallel runs are ok, and contrary to lapw0, the error does not occur for all cases (we did not notice any problem when testing the mpi benchmark with lapw1): w2k_dispatch_signal(): received: Segmentation fault application called MPI_Abort(MPI_COMM_WORLD, 768) - process 0 Our system is a Bullx DLC Cluster (LInux Red Hat+ Intel Ivybridge) and we use the compiler(+mkl) intel/14.0.2.144 and intelmpi/4.1.3.049. The batch Scheduler is SLURM. Here are the settings and the options we used for the installation : OPTIONS: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -Dmkl_scalapack -traceback -xAVX current:FFTW_OPT:-DFFTW3 -I/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/include current:FFTW_LIBS:-lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread current:RP_LIBS:-mkl=cluster -lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:MPIRUN:mpirun -np _NP_ _EXEC_ current:MKL_TARGET_ARCH:intel64 PARALLEL_OPTIONS: setenv TASKSET no setenv USE_REMOTE 1 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ _EXEC_ Any suggestions which could help us to solve this problem would be greatly appreciated. Best regards, Rémi Arras ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Problem when running MPI-parallel version of LAPW0
Hello Rémi,
While I'm not sure this is the (only) problem, in our setup we also give
mpirun the machines file:
setenv WIEN_MPIRUN mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
which I generate based on a 1 k-point per node setup with the following
python script:
/wienhybrid
#!/usr/bin/env python
#Machines file generator for WIEN2k
#May 13th 2013
#
#Michael Sluydts
#Center for Molecular Modeling
#Ghent University
from collections import Counter
import subprocess, os
nodefile = subprocess.Popen('echo
$PBS_NODEFILE',stdout=subprocess.PIPE,shell=True)
nodefile = nodefile.communicate()[0].strip()
nodefile = open(nodefile,'r')
machines = nodefile.readlines()
nodefile.close()
node = ''
corecount=Counter()
#gather cores per nodes
for core in machines:
node = core.split('.')[0]
corecount[node] += 1
#if there are more nodes than k-points we must redistribute the
remaining cores
#count the irreducible kpoints
IBZ = int(subprocess.Popen('wc -l ' + os.getcwd().split('/')[-1] +
'.klist',stdout=subprocess.PIPE,shell=True).communicate()[0])-2
corerank = corecount.most_common()
alloc = Counter()
total = Counter()
nodemap = []
#pick out the largest nodes and redivide the remaining ones by adding
the largest leftover node to the k-point with least allocated cores
for node,cores in corerank:
if len(alloc) IBZ:
alloc[node] += cores
total[node] += cores
else:
lowcore = total.most_common()[-1][0]
total[lowcore] += cores
nodemap.append((node,lowcore))
#give lapw0 all cores
machinesfile = 'lapw0: ' + corecount.keys()[0] + ':' +
str(corecount[corecount.keys()[0]]) + '\n'
#for node in corecount.keys():
#machinesfile += node + ':' + str(corecount[node]) + ' '
#machinesfile += '\n'
#machinesfile = ''
for node in alloc.keys():
#allocate main node
machinesfile += '1:' + node + ':' + str(alloc[node])
#machinesfile += '1:' + node
#for i in range(1,alloc[node]):
#machinesfile += ' ' + node
#distribute leftover nodes
extra = [x for x,y in nodemap if y == node]
for ext in extra:
#machinesfile += ' ' + ext + ':' + str(corecount[ext])
for i in range(1,corecount[ext]):
machinesfile+=' ' + ext
machinesfile += '\n'
#If your nodes do not all have the same specifications you may have to
change the weights above 1: and the granularity below, if you use a
residue machine you should remove extrafine and add the residue
configuration
machinesfile += 'granularity:1\nextrafine:1\n'
#if you have memory issues or a limited bandwidth between nodes try
uncommenting the following line (can always try it and see if it speeds
things up)
#machinesfile += 'lapw2 vector split:2\n'
machines = file('.machines','w')
machines.write(machinesfile)
machines.close()
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Re: [Wien] Problem when running MPI-parallel version of LAPW0
Perhaps an important note: the python script is for a Torque PBS queuing system (based on $PBS_NODEFILE) Rémi Arras schreef op 22/10/2014 13:29: Dear Pr. Blaha, Dear Wien2k users, We tried to install the last version of Wien2k (14.1) on a supercomputer and we are facing some troubles with the MPI parallel version. 1)lapw0 is running correctly in sequential, but crashes systematically when the parallel option is activated (independently of the number of cores we use): lapw0 -p(16:08:13) starting parallel lapw0 at lun. sept. 29 16:08:13 CEST 2014 .machine0 : 4 processors Child id1 SIGSEGV Child id2 SIGSEGV Child id3 SIGSEGV Child id0 SIGSEGV **lapw0 crashed! 0.029u 0.036s 0:50.91 0.0%0+0k 5248+104io 17pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed stop error w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault Child with myid of1has an error 'Unknown' - SIGSEGV Child id1 SIGSEGV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 **lapw0 crashed! cat: No match.0.027u 0.034s 1:33.13 0.0%0+0k 5200+96io 16pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed 2) lapw2 also crashes sometimes when MPI parallelization is used. Sequential or k-parallel runs are ok, and contrary to lapw0, the error does not occur for all cases (we did not notice any problem when testing the mpi benchmark with lapw1): w2k_dispatch_signal(): received: Segmentation fault application called MPI_Abort(MPI_COMM_WORLD, 768) - process 0 Our system is a Bullx DLC Cluster (LInux Red Hat+ Intel Ivybridge) and we use the compiler(+mkl) intel/14.0.2.144 and intelmpi/4.1.3.049. The batch Scheduler is SLURM. Here are the settings and the options we used for the installation : OPTIONS: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -Dmkl_scalapack -traceback -xAVX current:FFTW_OPT:-DFFTW3 -I/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/include current:FFTW_LIBS:-lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread current:RP_LIBS:-mkl=cluster -lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:MPIRUN:mpirun -np _NP_ _EXEC_ current:MKL_TARGET_ARCH:intel64 PARALLEL_OPTIONS: setenv TASKSET no setenv USE_REMOTE 1 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ _EXEC_ Any suggestions which could help us to solve this problem would be greatly appreciated. Best regards, Rémi Arras ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Problem when running MPI-parallel version of LAPW0
It is often hard to know exactly what issues are with mpi. Most often it is due to incorrect combinations of scalapack/blacs in the linking options. The first think to check is your linking options with https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/. What you have does not look exactly right to me, but I have not used your release. If that does not work, look in case.dayfile, the log file. If there is still nothing it is sometimes useful to comment out the line CALL W2kinit in lapw0.F, recompile then just do x lapw0 -p. You sometimes will get more information although it is not as safe as mpi tasks can hang forever without it in some cases. On Wed, Oct 22, 2014 at 6:29 AM, Rémi Arras remi.ar...@cemes.fr wrote: Dear Pr. Blaha, Dear Wien2k users, We tried to install the last version of Wien2k (14.1) on a supercomputer and we are facing some troubles with the MPI parallel version. 1) lapw0 is running correctly in sequential, but crashes systematically when the parallel option is activated (independently of the number of cores we use): lapw0 -p(16:08:13) starting parallel lapw0 at lun. sept. 29 16:08:13 CEST 2014 .machine0 : 4 processors Child id 1 SIGSEGV Child id 2 SIGSEGV Child id 3 SIGSEGV Child id 0 SIGSEGV ** lapw0 crashed! 0.029u 0.036s 0:50.91 0.0% 0+0k 5248+104io 17pf+0w error: command /eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.def failed stop error w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault Child with myid of1 has an error 'Unknown' - SIGSEGV Child id 1 SIGSEGV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 ** lapw0 crashed! cat: No match.0.027u 0.034s 1:33.13 0.0% 0+0k 5200+96io 16pf+0w error: command /eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.def failed 2) lapw2 also crashes sometimes when MPI parallelization is used. Sequential or k-parallel runs are ok, and contrary to lapw0, the error does not occur for all cases (we did not notice any problem when testing the mpi benchmark with lapw1): w2k_dispatch_signal(): received: Segmentation fault application called MPI_Abort(MPI_COMM_WORLD, 768) - process 0 Our system is a Bullx DLC Cluster (LInux Red Hat+ Intel Ivybridge) and we use the compiler(+mkl) intel/14.0.2.144 and intelmpi/4.1.3.049. The batch Scheduler is SLURM. Here are the settings and the options we used for the installation : OPTIONS: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -Dmkl_scalapack -traceback -xAVX current:FFTW_OPT:-DFFTW3 -I/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/include current:FFTW_LIBS:-lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread current:RP_LIBS:-mkl=cluster -lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:MPIRUN:mpirun -np _NP_ _EXEC_ current:MKL_TARGET_ARCH:intel64 PARALLEL_OPTIONS: setenv TASKSET no setenv USE_REMOTE 1 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ _EXEC_ Any suggestions which could help us to solve this problem would be greatly appreciated. Best regards, Rémi Arras -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: MURI4D.numis.northwestern.edu Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Problem when running MPI-parallel version of LAPW0
Usually the crucial point for lapw0 is the fftw3-library. I noticed you have fftw-3.3.4, which I never tested. Since fftw is incompatible between fftw2 and 3, maybe they have done something again ... Besides that, I assume you have installed fftw using the same ifor and mpi versions ... On 10/22/2014 01:29 PM, Rémi Arras wrote: Dear Pr. Blaha, Dear Wien2k users, We tried to install the last version of Wien2k (14.1) on a supercomputer and we are facing some troubles with the MPI parallel version. 1)lapw0 is running correctly in sequential, but crashes systematically when the parallel option is activated (independently of the number of cores we use): lapw0 -p(16:08:13) starting parallel lapw0 at lun. sept. 29 16:08:13 CEST 2014 .machine0 : 4 processors Child id1 SIGSEGV Child id2 SIGSEGV Child id3 SIGSEGV Child id0 SIGSEGV **lapw0 crashed! 0.029u 0.036s 0:50.91 0.0%0+0k 5248+104io 17pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed stop error w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault Child with myid of1has an error 'Unknown' - SIGSEGV Child id1 SIGSEGV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 **lapw0 crashed! cat: No match.0.027u 0.034s 1:33.13 0.0%0+0k 5200+96io 16pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed 2) lapw2 also crashes sometimes when MPI parallelization is used. Sequential or k-parallel runs are ok, and contrary to lapw0, the error does not occur for all cases (we did not notice any problem when testing the mpi benchmark with lapw1): w2k_dispatch_signal(): received: Segmentation fault application called MPI_Abort(MPI_COMM_WORLD, 768) - process 0 Our system is a Bullx DLC Cluster (LInux Red Hat+ Intel Ivybridge) and we use the compiler(+mkl) intel/14.0.2.144 and intelmpi/4.1.3.049. The batch Scheduler is SLURM. Here are the settings and the options we used for the installation : OPTIONS: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -Dmkl_scalapack -traceback -xAVX current:FFTW_OPT:-DFFTW3 -I/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/include current:FFTW_LIBS:-lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread current:RP_LIBS:-mkl=cluster -lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:MPIRUN:mpirun -np _NP_ _EXEC_ current:MKL_TARGET_ARCH:intel64 PARALLEL_OPTIONS: setenv TASKSET no setenv USE_REMOTE 1 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ _EXEC_ Any suggestions which could help us to solve this problem would be greatly appreciated. Best regards, Rémi Arras ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/staff/tc_group_e.php -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Wien Digest, Vol 107, Issue 6
+
Dear Victor,
Thank you for your answer, I know the concepts one by one (at least I
think I know), however, my question is still about their equalization,
for example, when we run an Anti ferromagnetic calculation in Wien2k
for a bulk system, which one of the Closed shell, open shell,
Restricted or unrestricted configuration would be really applied in
this case?
For example as I mentioned: A non-spin polarized calculation in
Wien2k(run_lapw) apparently looks like a closed shell system which
usually is used for nonmagnetic or Diamagnetic materials.
So, again what is important for me is approximate equalization of
these two groups of definition.
And it is always easy to understand to see how the orbital are filled
out for example in O2 molecule (in the gas phase or as a impurity in
large system)and predict the magnetic or spin ordering behavior of
O2 molecule, but it would be a bit challenging when we want to
explain for example Anti ferromagnetic behavior of NiO or
ferromagnetic behavior of Gd5Ge4, but not by plotting DOS or band
structure but by presenting the molecule orbitals exactly like what is
doing for O2 molecule.
Cheers,
Salman
+
Subject: [Wien] Bridging from Physics to Chemistry
+++
Dear Wien2k users,
I get always confused while bridging from Physics to Chemistry in
explaining spin and Magnetism.
So, I would be highly appreciated if anybody kindly equalized (if it
is possible)in DFT the concepts like Nonmagnetic, Paramagnetic,
Ferromagnetic, Anti-ferromagnetic and Ferrimagnetic in one hand
and Closed shell, Open shell, Spin restricted and Spin
unrestricted configurations in the another hand, specially in the
case of infinite system like an usual bulk (magnetic or nonmagnetic)
which is possible to be easily treated in a plane wave code like Wien2k.
To start, I can just say: doing a non-spin polarized calculation in
for example Wien2k (run_lapw) equals to a Closed shell calculation.
And also, for me a Ferrimagnetic looks like a Spin unrestricted
configuration ... .
Best regards,
Salman Zarrini
+++
You are asking an impressive list of things and it is not easy
to answer them. You would need a complete master course for this.
1) Let me start from the electronic structure concept of closed and open
shell. A closed shell corresponds to have all orbital levels empty or
containing a complete collection of electrons. So a ns(2), np(6), nd(10)
or nf(14) are closed shells. An open shell corresponds to have nl(N),
for 0N2*(2*l+1). Remember that in period n the nl orbitals are the
valence ones and the ones involved in chemical bonding.
Closed shells are electronic groups that belong to the fully symmetric
irreducible representation (irrep) for the local symetry group. So they
do not provide many energy levels to your system.
So, when you examine the optical properties of a Cr(+3) impurity in a
Al2O3 corundum crystal is the energy levels of the Cr(+3) open shell
the ones that produce the interesting optical properties. The Al(+3) and
O(-2) ions are closed shells and the provide the chemical ambient where
the 3d impurities do the nice things.
Similarly in the second and third transition metal atoms or in the nf
rare earths. All of them tend to produce rich open shell groups.
2) As for the cooperative magnetism of ferro, ferri, etc I advice you
to explore some good text on the subject: Tipler, Kittel, Ashcroft-Mermin.
The diffrent types of magnetism correspond to different couplings of the
m_s spins in neighbor unit cells of the crystal.
3) The spin restricted and unrestricted SCF techniques correspond
to force the alfa (m_s=+1/2) and beta (m_s=-1/2) electrons having
the same spacial description (restricted) or let the two groups
occupy different regions in space, i.e. different R_{nl}(r) and
R_{nl}^prime(r) orbitals. The unrestricted techniques are very important
as a first step in solving the correlation energy problem.
If you have been lost in this lengthy post don't worry. I told you that
your question was not easy.
Regards,
V?ctor Lua?a
--
\|/a After years of working on a problem the genius shout:
|^.^| what an idiot I am ... the solution is trivial!'
+-!OO--\_/--OO!--+---
!Dr.V?ctor Lua?a !
! Departamento de Qu?mica F?sica y Anal?tica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail: vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491 fax: +34-985-103125 !
+--+
GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)
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SEARCH the MAILING-LIST at:
[Wien] Bridging from Physics to Chemistry
+
Dear Victor,
Thank you for your answer, I know the concepts one by one (at least I
think I know), however, my question is still about their equalization,
for example, when we run an Anti ferromagnetic calculation in Wien2k
for a bulk system, which one of the Closed shell, open shell,
Restricted or unrestricted configuration would be really applied in
this case? For example as I mentioned: A non-spin polarized
calculation in Wien2k(run_lapw) apparently looks like a closed shell
system which usually is used for nonmagnetic or Diamagnetic materials.
So, again what is important for me is approximate equalization of
these two groups of definition. And it is always easy to understand to
see how the orbital are filled out for example in O2 molecule (in
the gas phase or as a impurity in large system)and predict the
magnetic or spin ordering behavior of O2 molecule, but it would be a
bit challenging when we want to explain for example Anti ferromagnetic
behavior of NiO or ferromagnetic behavior of Gd5Ge4, but not by
plotting DOS or band structure but by presenting the molecule orbitals
exactly like what is doing for O2 molecule.
Cheers,
Salman Zarrini
+
[Hide Quoted Text]
Subject: [Wien] Bridging from Physics to Chemistry
+++
Dear Wien2k users,
I get always confused while bridging from Physics to Chemistry in
explaining spin and Magnetism.
So, I would be highly appreciated if anybody kindly equalized (if it
is possible)in DFT the concepts like Nonmagnetic, Paramagnetic,
Ferromagnetic, Anti-ferromagnetic and Ferrimagnetic in one hand
and Closed shell, Open shell, Spin restricted and Spin
unrestricted configurations in the another hand, specially in the
case of infinite system like an usual bulk (magnetic or nonmagnetic)
which is possible to be easily treated in a plane wave code like Wien2k.
To start, I can just say: doing a non-spin polarized calculation in
for example Wien2k (run_lapw) equals to a Closed shell calculation.
And also, for me a Ferrimagnetic looks like a Spin unrestricted
configuration ... .
Best regards,
Salman Zarrini
+++
You are asking an impressive list of things and it is not easy
to answer them. You would need a complete master course for this.
1) Let me start from the electronic structure concept of closed and open
shell. A closed shell corresponds to have all orbital levels empty or
containing a complete collection of electrons. So a ns(2), np(6), nd(10)
or nf(14) are closed shells. An open shell corresponds to have nl(N),
for 0N2*(2*l+1). Remember that in period n the nl orbitals are the
valence ones and the ones involved in chemical bonding.
Closed shells are electronic groups that belong to the fully symmetric
irreducible representation (irrep) for the local symetry group. So they
do not provide many energy levels to your system.
So, when you examine the optical properties of a Cr(+3) impurity in a
Al2O3 corundum crystal is the energy levels of the Cr(+3) open shell
the ones that produce the interesting optical properties. The Al(+3) and
O(-2) ions are closed shells and the provide the chemical ambient where
the 3d impurities do the nice things.
Similarly in the second and third transition metal atoms or in the nf
rare earths. All of them tend to produce rich open shell groups.
2) As for the cooperative magnetism of ferro, ferri, etc I advice you
to explore some good text on the subject: Tipler, Kittel, Ashcroft-Mermin.
The diffrent types of magnetism correspond to different couplings of the
m_s spins in neighbor unit cells of the crystal.
3) The spin restricted and unrestricted SCF techniques correspond
to force the alfa (m_s=+1/2) and beta (m_s=-1/2) electrons having
the same spacial description (restricted) or let the two groups
occupy different regions in space, i.e. different R_{nl}(r) and
R_{nl}^prime(r) orbitals. The unrestricted techniques are very important
as a first step in solving the correlation energy problem.
If you have been lost in this lengthy post don't worry. I told you that
your question was not easy.
Regards,
V?ctor Lua?a
--
\|/a After years of working on a problem the genius shout:
|^.^| what an idiot I am ... the solution is trivial!'
+-!OO--\_/--OO!--+---
!Dr.V?ctor Lua?a !
! Departamento de Qu?mica F?sica y Anal?tica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail: vic...@fluor.quimica.uniovi.es !
! phone: +34-985-103491 fax: +34-985-103125 !
+--+
GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)
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Re: [Wien] Wien Digest, Vol 107, Issue 6
On Wed, Oct 22, 2014 at 02:31:15PM +0200, Salman Zarrini wrote: + Dear Victor, Thank you for your answer, I know the concepts one by one (at least I think I know), however, my question is still about their equalization, for example, when we run an Anti ferromagnetic calculation in Wien2k for a bulk system, which one of the Closed shell, open shell, I guess that you are a chemist (may I ask your main subject?) trying to follow a road to solid state physics. Wellcome to the road. May be you will find useful the book by Roald Hoffmann that tries to introduce chemists to solid state: Roald Hoffmann, Solid State Physics: An Introduction, 2nd ed http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527412824.html There is a book by Dronskowski devoted to computational methods: Computational Chemistry of Solid State Materials: A Guide for Materials Scientists, Chemists, Physicists and others by Richard Dronskowski http://eu.wiley.com/WileyCDA/Section/id-WILEYEUROPE2_SEARCH_RESULT.html?query=Dronskowski Regards, Dr. Víctor Luaña -- \|/a After years of working on a problem the genius shout: |^.^| what an idiot I am ... the solution is trivial!' +-!OO--\_/--OO!--+--- !Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: vic...@fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Wien Digest, Vol 107, Issue 6 (Bridging from Physics to Chemistry)
+++ My background is Physics but working in a Chemistry department where I have to always switch the language from Physics to Chemistry when I wanna discuss something which makes life a bit tough for me. Any way, thank you for the links, I think I have the one from Roald Hoffmann in my archive. Cheers, Salman Zarrini +++ I guess that you are a chemist (may I ask your main subject?) trying to follow a road to solid state physics. Wellcome to the road. May be you will find useful the book by Roald Hoffmann that tries to introduce chemists to solid state: Roald Hoffmann, Solid State Physics: An Introduction, 2nd ed http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527412824.html There is a book by Dronskowski devoted to computational methods: Computational Chemistry of Solid State Materials: A Guide for Materials Scientists, Chemists, Physicists and others by Richard Dronskowski http://eu.wiley.com/WileyCDA/Section/id-WILEYEUROPE2_SEARCH_RESULT.html?query=Dronskowski Regards, Dr. Víctor Luaña -- \|/a After years of working on a problem the genius shout: |^.^| what an idiot I am ... the solution is trivial!' +-!OO--\_/--OO!--+--- !Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: vic...@fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Bridging from Physics to Chemistry
It is a bit beyond the topics of the mailing list, but I still will try to contribute to your understanding hoping that I'm not getting oversimplifying: The terms closed and open shell in atoms/molecules usually means that you have only paired electrons (each atomic/molecular orbital is occupied by a spin-up AND dn electron), or also unpaired electrons. From this definition it is also clear that any atom/molecule with an odd number of electrons will be open-shell, and in an open-shell systems there is a net spin-magnetic moment since the number of up/dn electrons is (usually) different). In a bigger molecule you could have several unpaired electrons in different MOs, but the be arranged in different ways in spin-up or dn, and one usually classifies them by specifying the spin-multiplicity (singlet, duplet,triplet,...) And last but not least, one can make an approximation restrict spin-up and dn-orbitals to be the same or not (restricted/unrestricted). In solids things are a bit different: If all electrons are paired and we have an insulator/semiconductor, we talk about a diamagnet (=closed shell) and it implies again that the number of electrons is even. However, in contrast to atoms/molecules, we can have a paramagnetic METAL, which can have an odd number of electrons and still the up and dn-electrons are equal. This is a consequence of the large (infinite) number of atoms in a 3D solid and the resulting delocalization of the electronic states, so that ONE atom may have only a small fraction of an electron in a particular orbital (better a Bloch-state). So the Na atom is a open shell system with 1 unpaired electron, while metallic Na is a paramagnet (and we do run_lapw, i.e. forcing equal number and orbitals for up and dn spin). Also in a solid you can have unpaired electrons (take the metals Fe or Cr), but then these open shell solutions may differ in the way they have long-range order (something that does of course not exist in molecules). If the spins on all atoms point into the same direction, we speak about a ferromagnet (Fe), but they could also be antiferromagnetic (spin-up on one atom, spin-dn on the next,...) or even more complicated (spin-spirals, non-collinear (or canted), Cr you can consider as AFM (although, actually it has a long spin-spiral...). So for AFM-Cr we do a spin-unrestricted calculation with a total singlet (zero) spin/unit cell), while for ferromagnetic Fe the total spin is non-zero (note, Fe has a NON-INTEGER spin-moment of 2.2 uB, something which does (to my knowledge) not exist in a finite system. And last but not least, an Antiferromagnet in MO-language is a system where there are more occupied orbitals of spin-up on atom 1; but more of spin-dn on atom 2. Or if you like: When we do the O2 molecule in a periodic code using a big supercell, the triplet O2 molecular state is a ferromagnet, while the singlet state would be an antiferromagnet. Thank you for your answer, I know the concepts one by one (at least I think I know), however, my question is still about their equalization, for example, when we run an Anti ferromagnetic calculation in Wien2k for a bulk system, which one of the Closed shell, open shell, Restricted or unrestricted configuration would be really applied in this case? For example as I mentioned: A non-spin polarized calculation in Wien2k(run_lapw) apparently looks like a closed shell system which usually is used for nonmagnetic or Diamagnetic materials. So, again what is important for me is approximate equalization of these two groups of definition. And it is always easy to understand to see how the orbital are filled out for example in O2 molecule (in the gas phase or as a impurity in large system)and predict the magnetic or spin ordering behavior of O2 molecule, but it would be a bit challenging when we want to explain for example Anti ferromagnetic behavior of NiO or ferromagnetic behavior of Gd5Ge4, but not by plotting DOS or band structure but by presenting the molecule orbitals exactly like what is doing for O2 molecule. -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/staff/tc_group_e.php -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Bridging from Physics to Chemistry
Dear Prof. Blaha, Thank you for your prompt and nice answer. So can you confirm me please that, in comparison of a paramagnetic METAL and a antiferromagnetic solid I would say that paramagnetic METAL is a kind of a closed shell system while a antiferromagnetic solid is a open shell but both of them have zero spin/unit cell,singlet state or so to speak, a paramagnetic METAL is a singlet closed shell system but antiferromagnetic is a singlet open shell system. I have to more questions which your answer would be highly appreciated: 1. What happen in a bulk case that we start a scf spin-polarized calculation (runsp_lapw) where all the spin for example are aligned up in initialization (instgen_lapw - case.inst) but at the end no spin magnetic moment or a nonmagnetic system would be harvested. Means we started from a Open shell system (in this case triplet or even more) but the SCF finished by a closed shell system, is it meaningful such changes? 2. Do you think does it make sense talking about paramagnetic behavior or call a system paramagne in the DFT calculation? as in one hand the zero kelvin is the temperature considered in all the DFT level calculations and codes, and in another hand we know that paramagnetic behavior shows up at higher than specific temperatures like curie and neel in solid states Best regards, Salman Zarrini Quoting Peter Blaha pbl...@theochem.tuwien.ac.at: It is a bit beyond the topics of the mailing list, but I still will try to contribute to your understanding hoping that I'm not getting oversimplifying: The terms closed and open shell in atoms/molecules usually means that you have only paired electrons (each atomic/molecular orbital is occupied by a spin-up AND dn electron), or also unpaired electrons. From this definition it is also clear that any atom/molecule with an odd number of electrons will be open-shell, and in an open-shell systems there is a net spin-magnetic moment since the number of up/dn electrons is (usually) different). In a bigger molecule you could have several unpaired electrons in different MOs, but the be arranged in different ways in spin-up or dn, and one usually classifies them by specifying the spin-multiplicity (singlet, duplet,triplet,...) And last but not least, one can make an approximation restrict spin-up and dn-orbitals to be the same or not (restricted/unrestricted). In solids things are a bit different: If all electrons are paired and we have an insulator/semiconductor, we talk about a diamagnet (=closed shell) and it implies again that the number of electrons is even. However, in contrast to atoms/molecules, we can have a paramagnetic METAL, which can have an odd number of electrons and still the up and dn-electrons are equal. This is a consequence of the large (infinite) number of atoms in a 3D solid and the resulting delocalization of the electronic states, so that ONE atom may have only a small fraction of an electron in a particular orbital (better a Bloch-state). So the Na atom is a open shell system with 1 unpaired electron, while metallic Na is a paramagnet (and we do run_lapw, i.e. forcing equal number and orbitals for up and dn spin). Also in a solid you can have unpaired electrons (take the metals Fe or Cr), but then these open shell solutions may differ in the way they have long-range order (something that does of course not exist in molecules). If the spins on all atoms point into the same direction, we speak about a ferromagnet (Fe), but they could also be antiferromagnetic (spin-up on one atom, spin-dn on the next,...) or even more complicated (spin-spirals, non-collinear (or canted), Cr you can consider as AFM (although, actually it has a long spin-spiral...). So for AFM-Cr we do a spin-unrestricted calculation with a total singlet (zero) spin/unit cell), while for ferromagnetic Fe the total spin is non-zero (note, Fe has a NON-INTEGER spin-moment of 2.2 uB, something which does (to my knowledge) not exist in a finite system. And last but not least, an Antiferromagnet in MO-language is a system where there are more occupied orbitals of spin-up on atom 1; but more of spin-dn on atom 2. Or if you like: When we do the O2 molecule in a periodic code using a big supercell, the triplet O2 molecular state is a ferromagnet, while the singlet state would be an antiferromagnet. Thank you for your answer, I know the concepts one by one (at least I think I know), however, my question is still about their equalization, for example, when we run an Anti ferromagnetic calculation in Wien2k for a bulk system, which one of the Closed shell, open shell, Restricted or unrestricted configuration would be really applied in this case? For example as I mentioned: A non-spin polarized calculation in
