Mn doped SmFeO3 property prediction

pymatgen
,
1

I am trying to predict the magnetic order transformations in Mn doped SmFeO3 using the MagneticStructureEnumerator class. However I am getting the error [WinError 193] %1 is not a valid Win32 application. How do I resolve this issue?

Attached is the complete discription of the error

OSError Traceback (most recent call last)
in
37 from pymatgen.transformations.advanced_transformations import MagOrderingTransformation
38 mag_par = MagOrderingTransformation({“Sm3+”:5,“Fe3+”:5,“O2-”:0,“Mn3+”:4}, order_parameter=0.5)
—> 39 SmFeO3_Mn_Mag_new = mag_par.apply_transformation(SmFeO3_Mn_prop)
40 print(SmFeO3_Mn_Mag_new)

~\anaconda3\lib\site-packages\pymatgen\transformations\advanced_transformations.py in apply_transformation(self, structure, return_ranked_list)
940 t = EnumerateStructureTransformation(**enum_kwargs)
941
→ 942 alls = t.apply_transformation(structure, return_ranked_list=return_ranked_list)
943
944 # handle the fact that EnumerateStructureTransformation can either

~\anaconda3\lib\site-packages\pymatgen\transformations\advanced_transformations.py in apply_transformation(self, structure, return_ranked_list)
445 )
446 try:
→ 447 adaptor.run()
448 except EnumError:
449 warn(“Unable to enumerate for max_cell_size = {}”.format(max_cell_size))

~\anaconda3\lib\site-packages\pymatgen\command_line\enumlib_caller.py in run(self)
140 self._gen_input_file()
141 # Perform the actual enumeration
→ 142 num_structs = self._run_multienum()
143 # Read in the enumeration output as structures.
144 if num_structs > 0:

~\anaconda3\lib\site-packages\pymatgen\command_line\enumlib_caller.py in _run_multienum(self)
292 def _run_multienum(self):
293
→ 294 p = subprocess.Popen([enum_cmd],
295 stdout=subprocess.PIPE,
296 stdin=subprocess.PIPE, close_fds=True)

~\anaconda3\lib\subprocess.py in init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text)
852 encoding=encoding, errors=errors)
853
→ 854 self._execute_child(args, executable, preexec_fn, close_fds,
855 pass_fds, cwd, env,
856 startupinfo, creationflags, shell,

~\anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
1305 # Start the process
1306 try:
→ 1307 hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
1308 # no special security
1309 None, None,

OSError: [WinError 193] %1 is not a valid Win32 application

​

2

In the beginning of the file enumlib_caller.py it says

This module implements an interface to enumlib, Gus Hart’s excellent Fortran code for enumerating derivative structures.
This module depends on a compiled enumlib with the executables enum.x and makestr.x available in the path. Please download the library at GitHub - msg-byu/enumlib: Derivative structure enumeration library and follow the instructions in the README to compile these two executables accordingly.

I haven’t used this myself, but the error sounds like you haven’t compiled those?

-Peter

3

Thanks for your response.
I have compiled enumlibcaller and have also added the required files to the path.
Not including the files associated with enumlib leads to a different error altogether.

4

I see. Not sure then, but have you verified that enum.x runs correctly in your command line?

5

No not yet.Am trying to do this now. The reason I didnt test this initially was because a different error was being displayed when there were problems pertaining to the installation of enumlib related dependencies.

When I downloaded the 32 bit version of anaconda and ran the same program ,the same error is being displayed.

6

Hi Peter,thanks its almost sorted I compiled enum.x and makestr.x .However I am having a bit of difficulty appending them to my path in jupyter.Do I need to add them to my anaconda directory or another directory to integrate them with jupyter?

7

Great! If you add the directory where enum.x is located to your PYTHONPATH variable then it should work fine, I believe. If not, there are many solutions to this if you search on Google or StackOverflow. Good luck!
-Peter

8

OSError Traceback (most recent call last)
in
29 from pymatgen.transformations.advanced_transformations import MagOrderingTransformation
30 mag_par = MagOrderingTransformation({“Sm3+”:5,“Fe3+”:5,“O2-”:0,“Mn3+”:4}, order_parameter=0.5)
—> 31 SmFeO3_Mn_Mag_new = mag_par.apply_transformation(SmFeO3_Mn_prop)
32 print(SmFeO3_Mn_Mag_new)

~/anaconda3/lib/python3.7/site-packages/pymatgen/transformations/advanced_transformations.py in apply_transformation(self, structure, return_ranked_list)
943 t = EnumerateStructureTransformation(**enum_kwargs)
944
→ 945 alls = t.apply_transformation(structure, return_ranked_list=return_ranked_list)
946
947 # handle the fact that EnumerateStructureTransformation can either

~/anaconda3/lib/python3.7/site-packages/pymatgen/transformations/advanced_transformations.py in apply_transformation(self, structure, return_ranked_list)
455 )
456 try:
→ 457 adaptor.run()
458 except EnumError:
459 warnings.warn(“Unable to enumerate for max_cell_size = {}”.format(max_cell_size))

~/anaconda3/lib/python3.7/site-packages/pymatgen/command_line/enumlib_caller.py in run(self)
136 # Read in the enumeration output as structures.
137 if num_structs > 0:
→ 138 self.structures = self._get_structures(num_structs)
139 else:
140 raise EnumError(“Unable to enumerate structure.”)

~/anaconda3/lib/python3.7/site-packages/pymatgen/command_line/enumlib_caller.py in _get_structures(self, num_structs)
331 rs = subprocess.Popen([makestr_cmd] + options,
332 stdout=subprocess.PIPE,
→ 333 stdin=subprocess.PIPE, close_fds=True)
334 stdout, stderr = rs.communicate()
335 if stderr:

~/anaconda3/lib/python3.7/subprocess.py in init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text)
798 c2pread, c2pwrite,
799 errread, errwrite,
→ 800 restore_signals, start_new_session)
801 except:
802 # Cleanup if the child failed starting.

~/anaconda3/lib/python3.7/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1549 if errno_num == errno.ENOENT:
1550 err_msg += ': ’ + repr(err_filename)
→ 1551 raise child_exception_type(errno_num, err_msg, err_filename)
1552 raise child_exception_type(err_msg)
1553

OSError: [Errno 8] Exec format error: ‘/mnt/c/Users/k2/anaconda3/makeStr.py’

how might I resolve this?

9

Hi , I managed to get the code to work ,however there is a problem in the output ,It is returning a hexadecimal memory location instead of a list :-

<pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator object at 0x7f179de1cc90>

how do I resolve this?

10

Congrats on solving the previous issue! Could you share what you have done to solve the issue, in case someone else has a similar issue?

Regarding the new problem: Can you share your code? Which output do you want? It seems like you are printing out the Python object itself.

11

will share my solution after I successfully get the output .Its better to have everything in one post

I wish to print the output of the MagneticStructureEnumerator class i.e the proposed orderings in different strategies such as ferromagnetic ,paramagnetic etc.
My code is :-
import requests
response = requests.get(“https://www.materialsproject.org/rest/v2/materials/mp-1234/vasp”,
{“API_KEY”: “CLASSIFIED”})
from pymatgen.ext.matproj import MPRester
with MPRester(“CLASSIFIED”) as mpr:
SmFeO3 = mpr.get_structure_by_material_id(“mp-20243”)

from pymatgen.transformations.standard_transformations import AutoOxiStateDecorationTransformation
ox_trans = AutoOxiStateDecorationTransformation()
SmFeO3_ox = ox_trans.apply_transformation(SmFeO3)

from pymatgen.transformations.site_transformations import PartialRemoveSitesTransformation
part_mat = PartialRemoveSitesTransformation([[4], [7]],[1.0, 1.0],algo=0)
SmFeO3_part_mat = part_mat.apply_transformation(SmFeO3_ox)

from pymatgen.transformations.site_transformations import InsertSitesTransformation
Mn_dope = InsertSitesTransformation([“Mn3+”, “Mn3+”],[[0.5, 0.0, 0.0],[0.0, 0.5, 0.0]], coords_are_cartesian=False, validate_proximity=True)
SmFeO3_Mn_doped = Mn_dope.apply_transformation(SmFeO3_part_mat)

from pymatgen.transformations.site_transformations import AddSitePropertyTransformation
Mn_prop = AddSitePropertyTransformation({“magmom”: [0.009,0.009,0.009,0.009,5.0,5.0,4.361,4.36,0.174,0.173,0.174,0.173,0.174,0.184,0.174,0.185,0.174,0.184,0.174,0.185]})
SmFeO3_Mn_prop = Mn_prop.apply_transformation(SmFeO3_Mn_doped)

import pymatgen.command_line.enumlib_caller
from pymatgen.analysis.magnetism.analyzer import MagneticStructureEnumerator
mag = MagneticStructureEnumerator(SmFeO3_Mn_prop,default_magmoms={“Sm3+”:0.009 ,“Fe3+”:4.36 ,“Mn3+”:5.0 ,“O2-”:0.173},strategies=(‘ferromagnetic’, ‘antiferromagnetic’))
print(list(mag))

The output i am getting is ‘MagneticStructureEnumerator’ object is not iterable

12

I looked into the MagneticStructureEnumerator class and it’s indeed a bit confusing/misleading as it says it returns a list of structures, but it actually doesn’t. To get the structures, you need to instead replace the last line with

print(mag.ordered_structures)

There is also an ordered_structures_origins property in case you need that as well.

-Peter

13

Thanks a lot

14

Great, glad it worked! @ek_2k09, could you summarize how you solved your previous issues please, in case someone else faces a similar problem?

-Peter

15

To those who may face the same error , or those who may be getting started with pymatgen like I am :-

If you are using windows switch to linux for using pymatgen and its associated libraries.
Thats all.