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‎README.md‎

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@@ -18,111 +18,7 @@ pip install git+https://github.com/yuzie007/[email protected]
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## Usage and Tutorial
2020

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Here we consider the hypothetical case when Cu<sub>3</sub>Au with the L1<sub>2</sub> structure is regarded as a random configuration of the A1 (fcc) structure. You can find the input files in the `examples` directory.
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1. Create `FORCE_SETS` file for the structure (maybe including disordered chemical configuration)
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you want to investigate using ``phonopy`` in a usual way.
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Be careful that the number of the structures with atomic displacements to get `FORCE_SETS` can be huge (>100)
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for a disordered configuration.
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2. Create `FORCE_CONSTANTS` file from `FORCE_SETS` file using `phonopy` as
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```
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phonopy writefc.conf
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```
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where `writefc.conf` is a text file like
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```
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FORCE_CONSTANTS = WRITE
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DIM = 2 2 2
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```
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``DIM`` must be the same as that what you used to get `FORCE_SETS`.
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3. Prepare two VASP-POSCAR-type files, `POSCAR` and `POSCAR_ideal`.
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POSCAR includes the original chemical configuration, which may be disordered.
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```
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Cu Au
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1.00000000000000
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3.7530000000000001 0.0000000000000000 0.0000000000000000
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0.0000000000000000 3.7530000000000001 0.0000000000000000
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0.0000000000000000 0.0000000000000000 3.7530000000000001
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Cu Au
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3 1
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Direct
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0.0000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.5000000000000000
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0.5000000000000000 0.5000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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```
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Note that although `FORCE_CONSTANTS` may be obtained using relaxed atomic positions,
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here the positions must be the ideal ones.
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`POSCAR_ideal` is the ideal configuration, from which the crystallographic symmetry is extracted.
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```
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X
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1.00000000000000
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3.7530000000000001 0.0000000000000000 0.0000000000000000
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0.0000000000000000 3.7530000000000001 0.0000000000000000
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0.0000000000000000 0.0000000000000000 3.7530000000000001
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X
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4
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Direct
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0.0000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.5000000000000000
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0.5000000000000000 0.5000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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```
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In this file I recommend to use dummy symbols like 'X' to avoid confusion.
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4. Prepare ``band.conf`` file including something like
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```
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DIM = 2 2 2
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PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
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BAND = 0 0 0 0 1/2 1/2, 1 1/2 1/2 0 0 0 1/2 1/2 1/2
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BAND_POINTS = 101
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BAND_LABELS = \Gamma X \Gamma L
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FORCE_CONSTANTS = READ
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```
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The style is very similar to that of phonopy conf files, but be careful about the following tags.
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- `DIM` describes the expansion from the original POSCAR to the POSCARs with atomic displacements used to get `FORCE_SETS`.
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Therefore, this should be the same as the phonopy option when creating the structures with atomic displacements (1).
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- `PRIMITIVE_AXIS` is the conversion matrix from `POSCAR_ideal` to the primitive cell you expect.
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**Since v0.6.2:** We can also use `BAND = AUTO` like
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```
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DIM = 2 2 2
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PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
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BAND = AUTO
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BAND_POINTS = 101
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FORCE_CONSTANTS = READ
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```
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Internally, this uses [SeeK-path](https://seekpath.readthedocs.io/en/latest/) via phonopy.
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4. Run
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```
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upho_weights band.conf
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```
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You hopefully get `band.hdf5` file. Note that this file can be in the order of GB.
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5. Run
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```
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upho_sf --fpitch 0.01 -s 0.05 --function lorentzian --format text
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```
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You hopefully get `sf_E1.dat`, `sf_E2.dat`, and `sf_SR.dat` files.
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In these files:
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- `1st column`: distance in the reciprocal space
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- `2nd column`: frequencies
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- `3rd column`: values of spectral functions
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Further
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- `sf_E1.dat` has the element-pair-resolved spectral functions.
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- `sf_E2.dat` has the element-resolved spectral functions.
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- `sf_SR.dat` has the spectral functions decomposed by the small representations.
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6. Plot the spectral functions. You can refer to `plot.py` in the example directory. Hopefully you get the figure like below:
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![](examples/L12_Cu3Au/sf.orig.svg)
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See the `examples` directory.
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## Options (`upho_weights`)
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examples/L12_Cu3Au/FORCE_SETS renamed to examples/00.L12_Cu3Au/FORCE_SETS

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examples/L12_Cu3Au/POSCAR renamed to examples/00.L12_Cu3Au/POSCAR

File renamed without changes.

examples/L12_Cu3Au/POSCAR_ideal renamed to examples/00.L12_Cu3Au/POSCAR_ideal

File renamed without changes.

‎examples/00.L12_Cu3Au/README.md‎

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# Example for an ordered alloy
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Here we consider the hypothetical case when Cu<sub>3</sub>Au with the L1<sub>2</sub> structure is regarded as a random configuration of the A1 (fcc) structure. You can find the input files in the `examples` directory.
4+
5+
1. Create `FORCE_SETS` file for the structure (maybe including disordered chemical configuration)
6+
you want to investigate using ``phonopy`` in a usual way.
7+
Be careful that the number of the structures with atomic displacements to get `FORCE_SETS` can be huge (>100)
8+
for a disordered configuration.
9+
10+
2. Create `FORCE_CONSTANTS` file from `FORCE_SETS` file using `phonopy` as
11+
```
12+
phonopy writefc.conf
13+
```
14+
where `writefc.conf` is a text file like
15+
```
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FORCE_CONSTANTS = WRITE
17+
DIM = 2 2 2
18+
```
19+
``DIM`` must be the same as that what you used to get `FORCE_SETS`.
20+
21+
3. Prepare two VASP-POSCAR-type files, `POSCAR` and `POSCAR_ideal`.
22+
POSCAR includes the original chemical configuration, which may be disordered.
23+
```
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Cu Au
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1.00000000000000
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3.7530000000000001 0.0000000000000000 0.0000000000000000
27+
0.0000000000000000 3.7530000000000001 0.0000000000000000
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0.0000000000000000 0.0000000000000000 3.7530000000000001
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Cu Au
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3 1
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Direct
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0.0000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.5000000000000000
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0.5000000000000000 0.5000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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```
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Note that although `FORCE_CONSTANTS` may be obtained using relaxed atomic positions,
38+
here the positions must be the ideal ones.
39+
40+
`POSCAR_ideal` is the ideal configuration, from which the crystallographic symmetry is extracted.
41+
```
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X
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1.00000000000000
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3.7530000000000001 0.0000000000000000 0.0000000000000000
45+
0.0000000000000000 3.7530000000000001 0.0000000000000000
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0.0000000000000000 0.0000000000000000 3.7530000000000001
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X
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4
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Direct
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0.0000000000000000 0.5000000000000000 0.5000000000000000
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0.5000000000000000 0.0000000000000000 0.5000000000000000
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0.5000000000000000 0.5000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000
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```
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In this file I recommend to use dummy symbols like 'X' to avoid confusion.
56+
57+
4. Prepare ``band.conf`` file including something like
58+
```
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DIM = 2 2 2
60+
PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
61+
BAND = 0 0 0 0 1/2 1/2, 1 1/2 1/2 0 0 0 1/2 1/2 1/2
62+
BAND_POINTS = 101
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BAND_LABELS = \Gamma X \Gamma L
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FORCE_CONSTANTS = READ
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```
66+
The style is very similar to that of phonopy conf files, but be careful about the following tags.
67+
68+
- `DIM` describes the expansion from the original POSCAR to the POSCARs with atomic displacements used to get `FORCE_SETS`.
69+
Therefore, this should be the same as the phonopy option when creating the structures with atomic displacements (1).
70+
71+
- `PRIMITIVE_AXIS` is the conversion matrix from `POSCAR_ideal` to the primitive cell you expect.
72+
73+
**Since v0.6.2:** We can also use `BAND = AUTO` like
74+
```
75+
DIM = 2 2 2
76+
PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
77+
BAND = AUTO
78+
BAND_POINTS = 101
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FORCE_CONSTANTS = READ
80+
```
81+
Internally, this uses [SeeK-path](https://seekpath.readthedocs.io/en/latest/) via phonopy.
82+
83+
4. Run
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```
85+
upho_weights band.conf
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```
87+
You hopefully get `band.hdf5` file. Note that this file can be in the order of GB.
88+
89+
5. Run
90+
```
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upho_sf --fpitch 0.01 -s 0.05 --function lorentzian --format text
92+
```
93+
You hopefully get `sf_E1.dat`, `sf_E2.dat`, and `sf_SR.dat` files.
94+
In these files:
95+
- `1st column`: distance in the reciprocal space
96+
- `2nd column`: frequencies
97+
- `3rd column`: values of spectral functions
98+
99+
Further
100+
101+
- `sf_E1.dat` has the element-pair-resolved spectral functions.
102+
- `sf_E2.dat` has the element-resolved spectral functions.
103+
- `sf_SR.dat` has the spectral functions decomposed by the small representations.
104+
105+
6. Plot the spectral functions. You can refer to `plot.py` in the example directory. Hopefully you get the figure like below:
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107+
![](sf.orig.svg)

examples/L12_Cu3Au/band.conf renamed to examples/00.L12_Cu3Au/band.conf

File renamed without changes.

examples/L12_Cu3Au/plot.py renamed to examples/00.L12_Cu3Au/plot.py

File renamed without changes.

examples/L12_Cu3Au/sf.orig.svg renamed to examples/00.L12_Cu3Au/sf.orig.svg

File renamed without changes.

examples/L12_Cu3Au/writefc.conf renamed to examples/00.L12_Cu3Au/writefc.conf

File renamed without changes.

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