Dear Thuto,
the important statement in your output message is:
ImportError: No module named site
This usually happens if the python environment variable PYTHONHOME is not defined.
Please also check if the environment variable PYTHONPATH is defined and included in the PATH.
Yours sincerely,
Pasquale Pavone (exciting team)
Dear Pasquale
Thank you for the information.
In my bash shell I have set the environment variables as instructed in the exciting oxygen version:
#================================================================================================
#The following shell variables are required for executing scripts in the exciting project work
export EXCITINGROOT=/mnt/lustre/users/tmosuang/exciting
export EXCITINGTOOLS=$EXCITINGROOT/tools
#------------------------------------------------------------------------------------------------
export TIMEFORMAT=" Elapsed time = %0lR"
#------------------------------------------------------------------------------------------------
export WRITEMINMAX=“1”
#------------------------------------------------------------------------------------------------
export PYTHONPATH=$PYTHONPATH:$EXCITINGROOT/stm
export PATH=$PATH:$EXCITINGTOOLS:$EXCITINGROOT/bin:$EXCITINGTOOLS/stm
#================================================================================================
So how does one define the PYTHONHOME?
Sincerely
Thuto
Just to clarify, $PYTHONPATH does not go in the $PATH.
Looking at the script LATTICE-parameters.sh calls:
$EXCITINGTOOLS/exciting2sgroup.py input.xml sgroup.in
sgroup sgroup.in 1>sgroup.out 2>sgroup.err
and
exciting2sgroup.py contains
from lxml import etree as ET
from numpy import linalg as NL
import numpy as NU
import sys
import os
I had a quick look and I actually can’t see where sgroup is defined.
I also don’t see anything importing site.
@TMosuang could you please:
a) Point me towards sgroup
b) Try running these two commands manually:
$EXCITINGTOOLS/exciting2sgroup.py input.xml sgroup.in
sgroup sgroup.in 1>sgroup.out 2>sgroup.err
You can switch $EXCITINGTOOLS for the explicit path. Also make sure you have input.xml in the same directory.
The directory containing sgroup will need to be in your $PATH or just copy sgroup.in to whatever directory sgroup is in.
Cheers,
Alex
Thank you Alex for the information.
I did managed to generate sgroup.in file with Be hexagonal lattice parameters.
I also managed to generate the sgroup.out and sgroup.err files.
But these are generated independent of the LATTICE-parameters.sh script.
And when you call the script: LATTICE-parameters.sh input.xml, they are all wiped out.
The challenge is I can’t proceed with the Be General lattice optimization tutorial if the LATTICE-parameters.sh script does not generate the Bravais lattice parameters.
If I move to the following sript: OPTIMIZE-lattice.py this what I get:
[[email protected] Be_OPT]$ …/exciting/tools/LATTICE-parameters.sh input.xml
ImportError: No module named site
a b c alpha beta gamma
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
[[email protected] Be_OPT]$ python …/exciting/tools/OPTIMIZE-lattice.py
Please enter the exciting input file name: input.xml
ImportError: No module named site
... Oops error: degenerated basis
Now I’m just stucked, I can’t progress with the tutorial.
Any other ideas …?
Oh please
Thuto
Hi Thuto,
I talked to Pasquale. Turns out sgroup is an external program (which I wasn’t aware of). But regarding your specific problem:
Looking at the LATTICE-parameters.sh, the main calls in that script are:
$EXCITINGTOOLS/exciting2sgroup.py $IXML sgroup.in
sgroup sgroup.in 1>sgroup.out 2>sgroup.err
where $IXML=input.xml. The rest of the script just extracts values from the sgroup.out file.
So if you’re able to get the above calls to work manually, there is no reason the script shouldn’t also work. Have you confirmed input.xml is in the same directory as LATTICE-parameters.sh (or you call as LATTICE-parameters.sh path/to/input.xml' and that sgroup.in` is written to the same directory, following the script execution?
Which script call gives the ImportError? I can’t find an attempt to import that library in our python scripts, which suggests it’s imported by sgroup. Have you tried pip installing the site package?
Cheers,
Alex
Hi Alex,
I need to mention that the sgroup.in file has the following inside:
P
4.3000000000 4.2999798768 6.4500000000 90.0000000000 90.0000000000 120.0001548077
2
0.666670000 0.333330000 0.750000000
Be.xml
0.333330000 0.666670000 0.250000000
Be.xml
But sgroup.out file is just empty (i…e “sgroup.out” 0L, 0C)
And sgroup.err file has “Error: the main conditions not satisfied”
Any idea?
Thuto
Dear Thuto,
I think this problem has the same origin as the problem pointed out in another post.
In writing explicitly the components of the basis vectors (basevect) or the
coordinates of the atoms (in particular, is they are expressed in crystal coordinates),
one has to be sure that constants like 1/3, sqrt(2), sqrt(3), etc., are given with the correct
number of significant digits:
1/3 → 0.3333333333
sqrt(3) ->1.73205080757
sqrt(3)/2 → 0.86602540378
Doing this, one should get in your case (inside the file sgroup.in) something like:
P
4.3000000000 4.3000000000 6.4500000000 90.0000000000 90.0000000000 120.00000000
2
0.666666667 0.333333333 0.750000000
Be.xml
0.333333333 0.666666667 0.250000000
Be.xml
which should work fine as input of sgroup.
If you still have problems, please upload here your input file input.xml.
Pasquale Pavone (exciting team)
Dear Pasquale
Oh thank you, I managed to generate the Be hexagonal lattice parameters.
But when I proceed with OPTIMIZE-lattice.py I get the following:
[[email protected] Be_OPT]$ LATTICE-parameters.sh input.xml
ImportError: No module named site
Bravais lattice: Hexagonal
a b c alpha beta gamma
4.30000 4.30000 6.45000 90.00000 90.00000 120.00000
[[email protected] Be_OPT]$ python …/exciting/tools/OPTIMIZE-lattice.py
Please enter the exciting input file name: input.xml
ImportError: No module named site
... Oops error: degenerated basis
What could be problem now?
Thuto
Hi Thuto, could you post the content of the files sgroup.out and sgroup.err ?
After googling, ImportError: No module named site is a python package problem. I would try looking at some of the stack exchange answers
The sgroup.err is just an empty file with: “sgroup.err” 0L, 0C
Here are the fisrt lines of the sgroup.out:
Bravais lattice: Hexagonal
a b c
4.30000000 4.29999999 6.45000000
alpha beta gamma
90.00000000 90.00000000 120.00000011
===== Decomposition of new basis vectors over input basis =====
1.000000 0.000000 0.000000 <— 1
0.000000 1.000000 0.000000 <— 2
0.000000 0.000000 1.000000 <— 3
==== Number of atoms in cell: 2
==== Atom positions:
0.66666667 0.33333333 0.75000000
Be
0.33333333 0.66666667 0.25000000
Be
==== Nonequivalent atoms, point group for each sort: ====
Sort number: 1
Names of point group: -6m2 -6m2 D3h
New basis vectors for this point group:
1.0000 0.0000 0.0000 <— 1
0.0000 1.0000 0.0000 <— 2
0.0000 0.0000 1.0000 <— 3
Thuto
Greetings
Still on the volume optimization example:
In directory: ~/Be_OPT/VOL/
I’m trying to extract the equilibrium parameters using OPTIMIZE-lattice.py
This what I get:
python …/…/exciting/tools/OPTIMIZE-lattice.py
Traceback (most recent call last):
File “/mnt/lustre/users/tmosuang/exciting/tools/OPTIMIZE-analyze.py”, line 29, in
from lxml import etree as ET
ImportError: No module named lxml
Please assist
Thuto
Greetings once more
Still on the hexagonal crystal optimization,I am trying to extract the equilibrium parameters using the script: OPTIMIZE-lattice.py
But the script generates the output files: BM_eos.out; BM-optimized.xml, and energy-vs-volume.
The plot output files BM_eos.png and BM_eos.eps are not generated.
What could be the problem?
Here is the situation:
[[email protected] VOL]$ OPTIMIZE-lattice.py
Murnaghan or Birch-Murnaghan EOS: [M/B] B
=====================================================================
Fit accuracy:
Log(Final residue in [Ha]): -5.43
Final parameters:
E_min = -29.3609624 [Ha]
V_min = 106.5756 [Bohr^3]
B_0 = 123.041 [GPa]
B’ = 3.436
This application failed to start because it could not find or load the Qt platform plugin “xcb”
in “”.
Reinstalling the application may fix this problem.
[[email protected] VOL]$
Dear Thuto,
please check the link here. It could contain some hints for solving your problem.
Best,
Pasquale Pavone (exciting team)
Hi Alex,
I was trying to use OPTIMIZE-lattice.py on my system (Ubuntu 20.04.1) with exciting-oxygen and I got the following error
… Oops sh: 1: sgroup: not found
So I tried to go on the exciting website to download sgroup, however the link doesn’t seem to work.
Kind regards,
Luigi
Hi Luigo,
I can’t find any reference to downloading sgroup and its name is too generic to google for.
Perhaps @PasqualePavone can give specifics.
Clearly this dependency should be dropped, although I am not sure it will occur in time for the next release.
Cheers,
Alex
Hi Luigi,
where did you try to download sgroup on the exciting website? Try at the link:
[http://exciting.wdfiles.com/local--files/oxygen-elastic/adon_v1_0.tar.gz](download sgroup).
Best regards,
Pasquale Pavone
Hi Pasquale and Alex,
I don’t remember how I got to the link that didn’t work and I can’t really find it anymore.
Regarding sgroup itself: I downloaded it and ran the makefile. Now when I run OPTIMIZE-lattice.py sgroup works fine and correctly identifies the spacegroup of 2H MoS2. However, now when I run OPTIMIZE-lattice.py I get the following message
File “/home/Documents/EXCITING/exciting/tools/OPTIMIZE-setup.py”, line 400, in
OUTOBJ.write(ET.tostring(root, method =‘xml’,
TypeError: write() argument must be str, not bytes
I ran the script 2to3:
“2to3 -w OPTIMIZE-setup.py”
So I’m not sure what happened.
Thanks for the help above,
Kind regards,
Luigi
Kind of weird that it doesn’t work. Try changing line 400 to
output_xml_str = ET.tostring(root, method ='xml',
pretty_print =True ,
xml_declaration=False ,
encoding ='UTF-8')
OUTOBJ.write(output_xml_str.decode("utf-8") )
If that doesn’t work, I assume there’s some problem with the XML root. You should print output_xml_str and inspect what it is (it should be a string).
Cheers,
Alex