This package is a set of tools to determine, by means of ab initio simulations, the value of the coupling constants in a Heisenberg-like effective magnetic model for a given magnetic system.
To install the package, just run
python3 setup.py install
The package consists of these three command line programs:
*) bond_generator:
From an standard cif file, produces a new cif file containing information about the bonds that defines a Heisenberg magnetic effective model. If the input file has already information about bonds, the output file contains both the bonds in the input as well as the new generated bonds.
- usage: bond_generator [-h] [--discretization [value]] [--rmin [value]]
- [--rmax [value]] ciffile outfile
- positional arguments:
ciffile load atomic positions from a cif file outfile Name of the outputfile. If it is not provided, the
output is printed to the standard output.- optional arguments:
-h, --help show this help message and exit
- --discretization [value]
- the tolerance in considering two distances as the same.
--rmin [value] the minimal distance between atoms of the bond --rmax [value] the maximal distance between atoms of the bond
As an example, by run
bond_generator.py --rmin 0 --rmax 4.9 --discretization .02 example1.cif example1-nnn.cif
for the example1.cif file in the examples folder, example1-nnn.cif file is created. The model can be modified by hand by means of a plain text editor.
- *) optconfs
Generate spin configurations to determine the coupling constants of a model with minimal condition number
- usage: optconfs.py [-h] [--known [known configuration file]]
- [--start [start file]] [-n numconfs] [-u updatesize] [--it iterations] ciffile outfile
- positional arguments:
ciffile load atomic positions from a cif file outfile Name of the outputfile. If it is not provided, the
output is printed to the standard output.
- optional arguments:
-h, --help show this help message and exit - --known [known configuration file]
- file with the set of configurations that we want to increase
- --start [start file] A file containing an initial guess for the target
- configurations.
-n numconfs number of new configurations to be generated -u updatesize number of random configurations to be generate on each step --it iterations number of iterations
As an example, by run
optconfs example1-nnn.cif optconfs1.out
on the examples/example1-nnn.cif generated by bond_generator, the file optconfs1.out is created, containing a list of magnetic configurations from which energies the coefficient couplings can be estimated. The program also writes a recovery file example1-nnn-resume.tmp, which can be used to improve the magnetic configuration choice:
optconfs --start example1-nnn-resume.tmp example1-nnn.cif optconfs1.out
If we want to know what would be most profiteable magnetic configurations to be simulated once we have already simulated a given set of configurations, we run
optconfs --known optconfs1.out example1-nnn-resume.tmp example1-nnn.cif optconfs2.out
In this case, the program will try to provide the optimal configuration to be added to those in optconfs1.out. We can ask for an specific amount of new configurations throw the parameter -n.
*) evaluate_cc
From a set of energies and magnetic configurations, estimates the coupling constants of a model.
- usage: evaluate_cc.py [-h] [--tolerance [value]] [--showequations]
- ciffile [input file]
- positional arguments:
ciffile load atomic positions from a cif file. [input file] file containing evaluated energies and magnetic
configurations.- optional arguments:
-h, --help show this help message and exit --tolerance [value] Provides the estimated error for the energies. --showequations Prints the resulting equations.
Notice that in the input file, each line consists on the energy of a magnetic configuration, followed by the correspondent magnetic configuration as a list [0,1,0,...]. Anything after a # is considerer as a comment. For example, a possible input file would be
# Energy Configuration Label 143121.12 [0,0,0,0,0,0,0] # Ferro up 143121.02 [1,1,0,0,1,1,1] # Disorder1 143121.24 [1,0,1,1,1,1,0] # Disorder2 143121.12 [1,1,1,1,1,1,1] # Ferro down
As an example, by run
evaluate_cc example1-nnn.cif optconfs2-en.in
we obtain
Results:
E_0 = 1022.8 +/- 0.001
J3 = 0.000307570720896 * 1022.8 +/- 0.00592942475367 J2 = -0.00107262742797 * 1022.8 +/- 0.00592942475367 J4 = 0.00102985269196 * 1022.8 +/- 0.00592942475367 J1 = 0.000721874592622 * 1022.8 +/- 0.00592942475367
Error in Modeled Energy:
34.1666666667 170.833333333 68.3333333335 68.3333333329 34.1666666666 34.1666666666
an estimation of the coupling constants printed, according to the configurations and energies provided in the file optconfs2.in. The program also prints the list of differences between the input energies and the energies evaluated by the magnetic model for each configuration, relative to the tolerance. This is useful once we have a large enough number of evaluated configurations to check the validity of the effective magnetic model. If some differences result larger than 1, it implies that the proposed magnetic model is unable to reproduce the input spectrum.