lattice/pyerrors
1
0
Fork 0
mirror of https://github.com/fjosw/pyerrors.git synced 2025-05-15 20:13:41 +02:00
Code Issues Projects Releases Packages Wiki Activity

Merge branch 'develop' into documentation

Browse source
This commit is contained in:
fjosw 2022-01-21 14:54:32 +00:00
commit 773f85cf7f
2 changed files with 23 additions and 15 deletions
Download patch file Download diff file Expand all files Collapse all files

21
pyerrors/__init__.py
View file

@ -161,7 +161,7 @@ Passing arguments to the `gamma_method` still dominates over the dictionaries.
## Irregular Monte Carlo chains ## Irregular Monte Carlo chains
Irregular Monte Carlo chains can be initialized with the parameter `idl`. `Obs` objects defined on irregular Monte Carlo chains can be initialized with the parameter `idl`.
```python ```python
# Observable defined on configurations 20 to 519 # Observable defined on configurations 20 to 519
@ -187,6 +187,8 @@ obs3.details()
``` ```
`Obs` objects defined on regular and irregular histories of the same ensemble can be computed with each other and the correct error propagation and estimation is automatically taken care of.
**Warning:** Irregular Monte Carlo chains can result in odd patterns in the autocorrelation functions. **Warning:** Irregular Monte Carlo chains can result in odd patterns in the autocorrelation functions.
Make sure to check the autocorrelation time with e.g. `pyerrors.obs.Obs.plot_rho` or `pyerrors.obs.Obs.plot_tauint`. Make sure to check the autocorrelation time with e.g. `pyerrors.obs.Obs.plot_rho` or `pyerrors.obs.Obs.plot_tauint`.
@ -241,7 +243,7 @@ my_new_corr = 0.3 * my_corr[2] * my_corr * my_corr + 12 / my_corr
- `Corr.correlate` constructs a disconnected correlation function from the correlator and another `Corr` or `Obs` object. - `Corr.correlate` constructs a disconnected correlation function from the correlator and another `Corr` or `Obs` object.
- `Corr.reweight` reweights the correlator. - `Corr.reweight` reweights the correlator.
`pyerrors` can also handle matrices of correlation functions and extract energy states from these matrices via a generalized eigenvalue problem (see `pyerrors.correlators.Corr.GEVP). `pyerrors` can also handle matrices of correlation functions and extract energy states from these matrices via a generalized eigenvalue problem (see `pyerrors.correlators.Corr.GEVP`).
For the full API see `pyerrors.correlators.Corr`. For the full API see `pyerrors.correlators.Corr`.
@ -273,17 +275,26 @@ print(my_derived_cobs)
`pyerrors.roots` `pyerrors.roots`
# Matrix operations # Matrix operations
`pyerrors.linalg` `pyerrors` provides wrappers for `Obs`-valued matrix operations based on `numpy.linalg`. The supported functions include:
- `inv` for the matrix inverse.
- `cholseky` for the Cholesky decomposition.
- `det` for the matrix determinant.
- `eigh` for eigenvalues and eigenvectors of hermitean matrices.
- `eig` for eigenvalues of general matrices.
- `pinv` for the Moore-Penrose pseudoinverse.
- `svd` for the singular-value-decomposition.
For the full API see `pyerrors.linalg`.
# Export data # Export data
The preferred exported file format within `pyerrors` is The preferred exported file format within `pyerrors` is json.gz
## Jackknife samples ## Jackknife samples
For comparison with other analysis workflows `pyerrors` can generate jackknife samples from an `Obs` object or import jackknife samples into an `Obs` object. For comparison with other analysis workflows `pyerrors` can generate jackknife samples from an `Obs` object or import jackknife samples into an `Obs` object.
See `pyerrors.obs.Obs.export_jackknife` and `pyerrors.obs.import_jackknife` for details. See `pyerrors.obs.Obs.export_jackknife` and `pyerrors.obs.import_jackknife` for details.
# Input # Input
`pyerrors.input` `pyerrors` includes an `input` submodule in which input routines and parsers for the output of various numerical programs are contained. For details see `pyerrors.input`.
''' '''
from .obs import * from .obs import *
from .correlators import * from .correlators import *

17
pyerrors/input/misc.py
View file

@ -1,6 +1,3 @@
#!/usr/bin/env python
# coding: utf-8
import os import os
import fnmatch import fnmatch
import re import re
@ -12,11 +9,12 @@ from ..obs import Obs
def read_pbp(path, prefix, **kwargs): def read_pbp(path, prefix, **kwargs):
"""Read pbp format from given folder structure. Returns a list of length nrw """Read pbp format from given folder structure. Returns a list of length nrw
Keyword arguments Parameters
----------------- ----------
r_start -- list which contains the first config to be read for each replicum r_start : list
r_stop -- list which contains the last config to be read for each replicum list which contains the first config to be read for each replicum
r_stop : list
list which contains the last config to be read for each replicum
""" """
extract_nfct = 1 extract_nfct = 1
@ -66,7 +64,6 @@ def read_pbp(path, prefix, **kwargs):
tmp_array = [] tmp_array = []
with open(path + '/' + ls[rep], 'rb') as fp: with open(path + '/' + ls[rep], 'rb') as fp:
# header
t = fp.read(4) # number of reweighting factors t = fp.read(4) # number of reweighting factors
if rep == 0: if rep == 0:
nrw = struct.unpack('i', t)[0] nrw = struct.unpack('i', t)[0]
@ -74,7 +71,7 @@ def read_pbp(path, prefix, **kwargs):
deltas.append([]) deltas.append([])
else: else:
if nrw != struct.unpack('i', t)[0]: if nrw != struct.unpack('i', t)[0]:
raise Exception('Error: different number of reweighting factors for replicum', rep) raise Exception('Error: different number of factors for replicum', rep)
for k in range(nrw): for k in range(nrw):
tmp_array.append([]) tmp_array.append([])