I'm trying to calculate the ELF1,2,3D on a simple crystal (LiOH).

I wish to know what i have to do to perform a ELF without calculate everytime the groundstate, in other words, what is the key to resume STATE.OUT when you want to calculate the properties.

Thanks in advice!

F. G.

I downloaded the newest version of exciting! . Now I tried to calculate the first component of the optical tensor of Fe. For this I used the input file of the examples of Fe and I added the properties momentummatrix, dielectric and linresptensor (optcomp 1 1 1).

inputfile:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet href="inputtohtml.xsl" type="text/xsl"?>

<input xsi:noNamespaceSchemaLocation="../../xml/excitinginput.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsltpath="../../../xml/" scratchpath="/tmp/chm/1">
<title></title>
<structure speciespath="../../species/">
<crystal scale="2.708">
<basevect>1.0 1.0 -1.0</basevect>
<basevect> 1.0 -1.0 1.0</basevect>
<basevect> -1.0 1.0 1.0</basevect>
</crystal>
<species speciesfile="Fe.xml">
<atom coord="0.0 0.0 0.0" bfcmt="0.0 0.0 0.0"></atom>
</species>
</structure>
<groundstate vkloff="0.5 0.5 0.5" nempty="10" ngridk="10 10 10" mixer="lin">
<spin bfieldc="0.0 0.0 0.01" spinorb="false"></spin>
</groundstate>
<properties>
<bandstructure>
<plot1d>
<path steps="200">
<point coord="0.00000 0.00000 0.00000" label="GAMMA"></point>
<point coord="0.50000 0.50000 -0.50000" label="H"></point>
<point coord="0.50000 0.00000 0.00000" label="N"></point>
<point coord="0.00000 0.00000 0.00000" label="GAMMA"></point>
<point coord="0.25000 0.25000 0.25000" label="P"></point>
</path>
</plot1d>
</bandstructure>
<momentummatrix>
</momentummatrix>
<dielectric>
</dielectric>
<linresponsetensor>
<optcomp>1 1 1</optcomp>
</linresponsetensor>
</properties>
</input>

But after starting I only get a error message:

Info(writegeom):
EXCITING lattice vectors and atomic positions written to geometry.xml
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
excitingser 0826CECB Unknown Unknown Unknown
excitingser 08203AFB Unknown Unknown Unknown
excitingser 082C8DA2 Unknown Unknown Unknown

Stack trace terminated abnormally.

Can you explain, why it does not work.
Thank you

Svenja Vollmar

I've adapted the example Fe input.xml file to my material system - MnSb. It is a double hexagonal crystal of the NiAs type. I have included all of the atoms, specified the basis vectors and all other necessary variables. I have attempted to run the input file with increasingly fewer things to calculate - getting down to just the groundstate - and yet the input file doesn't run. All I get is:

 PARSE_ERR 81 runParser abort: 

There is no reason that I can see in my input file for this error message. This new input file (copied in full below) is in a new directory in examples/, so the relative paths to the xml and species directories are the same as for Fe, and all the other example input.xml files.

I think this highlights however why I feel that informative error messages are absolutely vital. The above error message is next to useless as it provides no information to the user as to what is wrong, which part of the input file it cannot parse and give indications on how to correct the error. (Although the last part isn't necessary the first two are hugely important.)

Anyway, I really need to get this to work, so any help would, as always, be hugely appreciated.

 <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet href="inputtohtml.xsl" type="text/xsl"?> <input xsi:noNamespaceSchemaLocation="../../xml/excitinginput.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsltpath="../../../xml/"> <title></title> <structure speciespath="../../species/"> <crystal scale="4.128"> <basevect> 0.8660 0.5000 0.0000</basevect> <basevect>-0.8669 0.5000 0.0000</basevect> <basevect> 0.0000 0.0000 1.4024</basevect> </crystal> <species speciesfile="Mn_Jim.xml"> <atom coord="0.0 0.0 0.0" bfcmt="0.0 0.0 0.0"></atom> <atom coord="0.0 0.0 0.5" bfcmt="0.0 0.0 0.0"></atom> <species speciesfile="Sb_Jim.xml"> <atom coord=" 0.2887 0.5000 0.3506" bfcmt="0.0 0.0 0.0"></atom> <atom coord="-0.2887 0.5000 1.0518" bfcmt="0.0 0.0 0.0"></atom> </species> </structure> <groundstate vkloff="0.5 0.5 0.5" nempty="10" ngridk="5 5 5"> <spin bfieldc="0.0 0.0 0.01" spinorb="true"></spin> </groundstate> <properties> <bandstructure> <plot1d> <path steps="200"> <point coord="0.00000 0.00000 0.00000" label="GAMMA"></point> <point coord="1.00000 0.50000 0.00000" label="M"></point> <point coord="1.00000 0.00000 0.00000" label="K"></point> <point coord="0.00000 0.00000 0.00000" label="GAMMA"></point> <point coord="0.00000 0.00000 0.50000" label="A"></point> <point coord="1.00000 0.50000 0.50000" label="L"></point> <point coord="1.00000 0.00000 0.50000" label="H"></point> <point coord="0.00000 0.00000 0.50000" label="A"></point> </path> </plot1d> </bandstructure> <dos/> </properties> </input> 

I tried a 64 atoms supercell calculation with 8x8x8 k-point grid. There was the following error message :

excitingmpi(36114) malloc: * mmap(size=2405527552) failed (error code=12)
* error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
At line 197 of file ../../src/init1.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
Operating system error: Cannot allocate memory
Memory allocation failed

when I add either -g -ftrace=full or frame, I have the following error message :

excitingmpi(27612) malloc: * mmap(size=2405527552) failed (error code=12)
* error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
At line 197 of file ../../src/init1.f90
Traceback: (Innermost first)
Called from line 45 of file ../../src/gndstate.f90
Called from line 31 of file ../../src/src_inputparser/tasklauncher.f90
Called from line 21 of file ../../src/mainxml/main.f90
Operating system error: Cannot allocate memory
Memory allocation failed

mpirun has exited due to process rank 5 with PID 27612 on
node supernano.physics.uiowa.edu exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

The critical lines are :

The critical line is this:

init1.f90:197 allocate(sfacgk(ngkmax, natmtot, nspnfv, nkpt))

which is where the allocation failure occurs. From the mpi communication:

gndstate.f90: call MPI_Bcast(sfacgk, size(sfacgk), MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)

it appears that sfacgk is *not* split up among the different processes, but rather each process has a complete copy of sfacgk. Is it correct, and if it is a bug or was intentional?

Best,

Thomas

I have some problems to install EXCITING with g95 -m64 (it compiles in 32 bit architecture but I need the 64 arch to overcome the memory allocation limitation for fortran 32 bits on Mac). Here is the compiler lines in make.inc :
F90=/home/chanier/G95/g95-install/bin/i386-apple-darwin8.11.1-g95
F77=$(F90)
F90_OPTS = -O3 -m64
F77_OPTS = -O3 -freal-loops -m64
CPP_ON_OPT = -cpp -DXS -DISO -DTETRA

I have the following error message when I run make :

F90=/home/chanier/G95/g95-install/bin/i386-apple-darwin8.11.1-g95
F77=$(F90)
F90_OPTS = -O3 -m64
F77_OPTS = -O3 -freal-loops -m64
CPP_ON_OPT = -cpp -DXS -DISO -DTETRA

Do you have any idea to overcome the problem? Thank you for your help.

Thomas

I am experiencing some difficulties to install EXCITING on Mac Snow Leopard, with gfortran compiler and openmpi. The code compilation is OK, apparently, it issues at the end the executable excitingser and excitingmpi. The problem is that when I run exciting for the simple case of Ag (input file given in the example directory), it issues directly a Segmentation Fault without running.
Here is my make.inc file:

#############################
F90=gfortran
F77=$(F90)
F90_OPTS =# -g -DEBUG #-O2
F77_OPTS = # -O2 -freal-loops
CPP_ON_OPT = -cpp -DXS -DISO -DTETRA
LIB_ARP =libarpack.a
LIB_LPK = -L./ -llapack -lblas
LIB_FFT = -L./ fftlib.a
LIB_BZINT= libbzint.a
#####################################
LIBS= $(LIB_ARP) $(LIB_LPK) $(LIB_FFT) $(LIB_BZINT)

F90_DEBUGOPTS=-g -ftrace=full
F77_DEBUGOPTS=-g -ftrace=full

#Ignore if you don't have MPI or smplibs

MPIF90=/sw/openmpi/bin/mpif90
MPIF90_OPTS= $(F90_OPTS) $(CPP_ON_OPT) -DMPI -DMPIRHO -DMPISEC

F77MT=$(F77)
F90MT=$(F90)

SMP_LIBS=
SMPF90_OPTS=$(F90_OPTS)
SMPF77_OPTS=$(SMPF90_OPTS)

BUILDMPI=true
BUILDSMP=false

Do you have any idea to solve this problem?

best regards,

Thomas Chanier

I've just installed the latest version of exciting on a linux machine running ifort 9.1. When installing, I simply copied the ifort make.inc. I'm not looking at MPI or SMP yet. No other changes.

When I run the tests (again, simply running the Makefile without changes), several tests fail as shown below. I take it that's bad news. I haven't tried to do anything different yet - hoping someone has advice on what to try first.

Thanks!

Kevin

[jorissen@raphael exciting]$ more test/report/all.xml
<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet href="./report.xsl" type="text/xsl"?>
<report>
<test>
<name>Broydenfile S rwtest</name>
<description>- - </description>
<directory>test04</directory>
<status>passed</status>
</test>
<test>
<name>Broydenfile Y rwtest</name>
<description>- - </description>
<directory>test04</directory>
<status>passed</status>
</test>
<test>
<name>Eigenvalues_same_as_reference_file</name>
<description>The test is passed if the eigenvalues differ
less than 1e-05 between runlapack/EIGVAL.OUT and reference file reference/EIGVAL.OUT
difference=0</description>
<directory>test02/ </directory>
<status>passed</status>
</test>
<test>
<name>Pulay mixing works</name>
<description>The test run using pulay (3) finished without errors</description>
<directory>test03/runmixer3</directory>
<status>failed</status>
</test>
<test>
<name>arpack run</name>
<description>The arpack solver was correctly invoked</description>
<directory>test02/runarp</directory>
<status>passed</status>
</test>
<test>
<name>check iteration number of Al</name>
<description>iterations is 18 reference is 17</description>
<directory>test03/run</directory>
<status>failed</status>
</test>
<test>
<name>check iteration number of Al for Pulay mixing (3) </name>
<description>iterations is 10 reference is 10</description>
<directory>test03/runmixer2</directory>
<status>passed</status>
</test>
<test>
<name>check iteration number of Al for mixer2</name>
<description>iterations is 3 reference is 10</description>
<directory>test03/runmixer2</directory>
<status>passed</status>
</test>
<test>
<name>debug binary run</name>
<description>The test run standard mixing finished without errors</description>
<directory>test03/run</directory>
<status>failed</status>
</test>
<test>
<name>debug binary run mixer2</name>
<description>The test run using multicecant broyden finished without errors</description>
<directory>test03/runmixer2</directory>
<status>failed</status>
</test>
<test>
<name>eigenvalue_comparison_LAPACK ARPACK </name>
<description>The test is passed if the eigenvalues differ
less than 1e-05 between lapack and Arpack
difference=0.1599309358</description>
<directory>test02/ </directory>
<status>failed</status>
</test>
<test>
<name>is_it_Pulay</name>
<description>Pulay Mixing is used</description>
<directory>test03/runmixer3</directory>
<status>passed</status>
</test>
<test>
<name>is_it_linadapt</name>
<description>linadapt mixer was invoked</description>
<directory>test03/run</directory>
<status>passed</status>
</test>
<test>
<name>is_it_msec</name>
<description>used msec</description>
<directory>test03/runmixer2</directory>
<status>failed</status>
</test>
<test>
<name>lapack_run</name>
<description>The test run using lapack finished without errors</description>
<directory>test02/runlapack</directory>
<status>failed</status>
</test>
<test>
<name>totalenergy_compare_LAPACK_ARPACK </name>
<description>The test is passed if the total energy differs
less than 1e-07 between lapack and Arpack
difference=-5.42000009318144e-07</description>
<directory>test02/ </directory>
<status>failed</status>
</test>
</report>
[jorissen@raphael exciting]$

The error occurs just after the beginning of the first SCF iteration in the second optimization cykle. The last lines of INFO.OUT look like this:

Maximum force magnitude (target) : 0.8854817892E-03 ( 0.4999999874E-04)

+------+
| Updated atomic positions |
+------+

Species : 1 (Mg)
atomic positions (lattice) :
1 : 0.00000000 0.00000000 0.00000000
2 : 0.50000000 0.50000000 0.50000000

Species : 2 (H)
atomic positions (lattice) :
1 : 0.00000000 0.30411459 0.30411459
2 : 0.00000000 0.69588541 0.69588541
3 : 0.50000000 0.19588541 0.80411459
4 : 0.50000000 0.80411459 0.19588541

+------+
| Self-consistent loop started |
+------+

+-----+
| Iteration number : 1 |
+-----+

Using advanced method for search of linearization energies

I can send you the results of strace it you want. the input file goes below:

<title>MgH2</title>
<structure primcell="true" speciespath="../../source/species/">
<symmetries HermannMauguinSymbol="P42/mnm" HallSymbol="-P 4n 2n" SchoenfliesSymbol="D4h^14" spaceGroupNumber="D4h^14">
<lattice a="8.58018" b="8.58018" c="5.71567" ab="90.0" ac="90.0" bc="90.0"></lattice>
<WyckoffPositions>
<wspecies speciesfile="Mg.xml">
<wpos coord="0.000000000 0.000000000 0.000000000"/>
</wspecies>
<wspecies speciesfile="H.xml">
<wpos coord="0.3041000000 0.3041000000 0.000000000"/>
</wspecies>
</WyckoffPositions>
</symmetries>
<crystal>
<basevect>8.58018 0.00000 0.00000</basevect>
<basevect>0.00000 8.58018 0.00000</basevect>
<basevect>0.00000 0.00000 5.71567</basevect>
</crystal>
<species speciesfile="Mg_natanzon.xml">
<atom coord="0.0000 0.0000 0.0000"/>
<atom coord="0.5000 0.5000 0.5000"/>
</species>
<species speciesfile="H_natanzon.xml">
<atom coord="0.3041 0.3041 0.0000"/>
<atom coord="0.6959 0.6959 0.0000"/>
<atom coord="0.1959 0.8041 0.5000"/>
<atom coord="0.8041 0.1959 0.5000"/>
</species>
</structure>
<structureoptimization resume="true"></structureoptimization>
<groundstate ngridk="3 3 5" rgkmax="6" chgexs="0" xctype="GGAPerdew-Burke-Ernzerhof"></groundstate>
</input>

$ ../../source/bin/excitingser
»»> unrecognized attribute:
ldapu="FullyLocalisedLimit" in element groundstate

I've tried ldapu="1" and even ldapu="none", but with no success. But after looking at the code it seems that LDA+U is implemented, so could you suggest how I can use it?

Another question not related to this topic is how I can introduce the charge defects in the cell? does chgexs="+1" correspond to a cell with an electron added or removed? You have the positive electron charge, so I can't well understand how it is related to the charge of the cell. Also, in Wien2k if one needs to remove an electron it changes the number of valence electrons in case.in2 and adds the background charge in mixer. What about exciting, I cannot find where I can change the number of electrons, so I just change chgexs parameter, but does it really changes the electron number or it is a kind of background charge?

Thank you in advance for the help,
Yurko.

I've had a look at the Al example that comes with the exciting source code. I see that the following high symmetry points are defined in the input file:

  <point coord=" 0.75000 0.50000 0.25000" label="W" /> <point coord=" 0.50000 0.50000 0.50000" label="L" /> <point coord=" 0.00000 0.00000 0.00000" label="GAMMA" /> <point coord=" 0.50000 0.50000 0.00000" label="X" /> <point coord=" 0.75000 0.50000 0.25000" label="W" /> <point coord=" 0.75000 0.37500 0.37500" label="K" /> 

but I cannot seem to tally these co-ordinates with those in the Brillouin zone. The gamma point is at the centre of the zone and is being taken as the origin, but I'm having difficulty in figuring out why the other points have their specified locations. As I understand it, the gamma, K, x and w points are all co-planar, but each have different values of 'z'. I also understand that the x point is taken to be at the centre of a square face in the Brillouin zone and along the y-direction but that doesn't seem to be the case here.

I have tried to determine the band structure of my material (MnSb) which is a hexagonal crystal but the points that I have used do not seem to be high symmetry points and, frankly, the plotted band structure is a mess! The following are the co-ordinates that I use:

  <point coord="0.00000 0.00000 0.00000" label="GAMMA" ></point> <point coord="0.75000 0.43300 0.00000" label="M" ></point> <point coord="1.00000 0.00000 0.00000" label="K"></point> <point coord="0.00000 0.00000 0.00000" label="GAMMA" ></point> <point coord="0.00000 0.00000 1.00000" label="A" ></point> <point coord="0.75000 0.43330 1.00000" label="L" ></point> <point coord="1.00000 0.00000 1.00000" label="H" ></point> 

I calculated these co-ordinates with James Annett during last year's Psi-k DFT workshop held at Bristol University. We were happy that, given the definition of the gamma point being the origin and the location of the high symmetry points given at http://www.ioffe.ru/SVA/NSM/Semicond/Append/figs/fmd21_5.gif that these co-ordinates were correct, but that does not seem to be the case.

So, my questions are: how were the aluminium high symmetry points determined and what are the corresponding points for the hexagonal Brillouin zone?

Kind regards,
James

I would like to know if the TDDFT within the EXCITING code can address infinite system with 3D periodic boundary condition.

Thank you in anticipation,

Best,

Thomas Chanier

The .agr files open up OK in xmgrace version 5 (I have that installed on my local laptop and home PC) but the same file will not open on the remote computer cluster which runs xmgrace version 6. The given error is:

  syntax error: PAGE RESIZE 600, 600 Failed loading project file 

I also appreciate that this isn't strictly an Exciting problem, but I felt like it should be mentioned as other people may encounter this same problem.

I guess it is possible that the syntax has changed between versions, and it is also possible that the version of xmgrace on our computer cluster may be borked. I will check this out by installing version 6 on my local machine, but I wondered if anyone knew for definite before I set about investigating this problem as I really have very little experience with xmgrace.

the compilation with mpiifort fails at OEP

let me give you some details: (no external linear algebra libraries (lapack, blas, arpack) used whatsoever, only local ones,
all contaied within exciting)

- sequential compilation with this compiler is OK!: compilation with ifort 11.1 (exactly the same compiler than above, but this time MPI is off
(smp off as well) works fine and also runs the tests fine -having said that, the right version is 11.0.069, since i tried 11.0.081 as well, and the latter does not work-

- after switching on the MPI option, i had to create a new entry under platforms (in build) and simply
changed "mpif90" by "mpiifort" in order to get the right make.inc containing mpiifort
This set up seems to start fine the compilation with mpiifort, but once it gets into OEP it fails:

i am not sure this is related, but it looks like there is a precompiler directive MPIEXX that should be there (according to the code)
but the set up does not seem to put it there, is this correct?
(i am sending the exact error message in another message)

otherwise, will you please let me know where the problem could be

thanks

M Perez Jigato
KU Leuven

PS probably another detail could be of interest: the main reason i do not use mpif90 is that i have open-MPI in
my computer set up for gfortran, and that takes mpif90. Furthermore, when i try to compile with gfortran and mpif90
from open-MPI, after several code little changes, i get it to start compiling fine, but surprise!, once it gets into OEP,
it fails exactly at the same place and with the same error message than with mpiifort

Has anyone tried to calculate adsorption energies with exciting? I would like to calculate the adsorption energy of a hydrogen atom on a (2x2) Ru(0001) surface consisting of 4 layers using PBE. So, I need to do three calculations: Eads=E(HRu)-E(H)-E(Ru). Since I am only interested in an energy difference, I should get a lot of error cancellation, so I think something like 6x6x1 k-points should do. Can exciting do this (16 Ru atoms plus one H atom)?

I would like to use the adsorption energy as the *correct* value without any pseudopotential errors or basis set errors and compare this number with what I get from other DFT codes. Is this realistic?

Jens Jørgen

When I compile the SMP lib binary, I get the following:

make[1]: Entering directory ‘/home/spja/src/exciting/build/smp’
make -f ../Make.common
make[2]: Entering directory ‘/home/spja/src/exciting/build/smp’
../../utilities/mkmf -t ./template -f -m Makefile.libbzint -p libbzint.a ../../src/libbzint && make -f Makefile.libbzint libbzint.a
…………………………………………………………………. Makefile.libbzint is ready.
make[3]: Entering directory ‘/home/spja/src/exciting/build/smp’
template:3: * Recursive variable ‘FC’ references itself (eventually). Stop.
make[3]: Leaving directory ‘/home/spja/src/exciting/build/smp’
make[2]: * [libbzint.a] Error 2
make[2]: Leaving directory ‘/home/spja/src/exciting/build/smp’
make[1]: * [all] Error 2
make[1]: Leaving directory ‘/home/spja/src/exciting/build/smp’
make: * [smp] Error 2

Any thoughts or suggestions?

• The caveat: When compiling the parallel/MPI code, I have to edit the make.inc file to add the -fpp option. Failing to do that causes the compiler to throw a wobbly with numerous "# bad preprocessor" errors.