Merge branch 'develop' into feature/rwf

CHANGELOG.md

@@ -2,30 +2,39 @@
 
 All notable changes to this project will be documented in this file.
 
-## [2.0.0] - 2021-??-??
+## [2.0.0] - 2022-??-??
 ### Added
+- The possibility to work with Monte Carlo histories which are evenly or unevenly spaced was added.
+- `cov_Obs` added as a possibility to propagate the error of non Monte Carlo data together with Monte Carlo data.
 - `CObs` class added which can handle complex valued Markov chain Monte Carlo data and the corresponding error propagation.
 - Matrix to matrix operations like the matrix inverse now also work for complex matrices and matrices containing entries that are not `Obs` but `float` or `int`.
-- The possibility to work with Monte Carlo histories which are evenly or unevenly spaced was added.
+- Support for a new `json.gz` file format was added
 - The Corr class now has additional methods like `reverse`, `T_symmetry`, `correlate` and `reweight`.
-- `linalg` module now has explicit functions `inv` and `cholesky`.
+- `Corr.m_eff` can now cope with periodic and anti-periodic correlation functions
+- Forward, backward and improved variants of the first and second derivative were added to the `Corr` class
+- The `linalg` module now has explicit functions `inv` and `cholesky`.
 - `Obs` objects now have methods `is_zero` and `is_zero_within_error` as well as overloaded comparison operations.
 - Functions to convert Obs data to or from jackknife was added.
 - Alternative matrix multiplication routine `jack_matmul` was added to `linalg` module which makes use of the jackknife approximation and is much faster for large matrices.
 - Additional input routines for npr data added to `input.hadrons`.
+- The `sfcf` and `openQCD` input modules can now handle all recent file type versions.
+- `extract_t0` can now visualize the extraction on the fly
+- Module added which provides the Dirac gamma matrices in the Grid convention.
 - Version number added.
 
 ### Changed
 - The internal bookkeeping system for ensembles/replica was changed. The separator for replica is now `|`.
 - The fit functions were renamed to `least_squares` and `total_least_squares`.
+- The output of the fit functions is now a dedicated results class which keeps track of all relevant information
 - The fit functions can now deal with provided covariance matrices.
 - The convention for the fit range in the Corr class has been changed.
-- Obs.print was renamed to Obs.details and the output was improved.
+- Various method of the `Corr` class were renamed
+- `Obs.print` was renamed to `Obs.details` and the output was improved.
 - The default value for `Corr.prange` is now `None`.
 - The `input` module was restructured to contain one submodule per data source.
 - Performance of Obs.__init__ improved.
 
-### Deprecated
+### Removed
 - The function `plot_corrs` was deprecated as all its functionality is now contained within `Corr.show`
 - The kwarg `bias_correction` in `derived_observable` was removed
 - Obs no longer have an attribute `e_Q`

pyerrors/correlators.py

@@ -376,6 +376,24 @@ class Corr:
         """Reverse the time ordering of the Corr"""
         return Corr(self.content[:: -1])
 
+    def thin(self, spacing=2, offset=0):
+        """Thin out a correlator to suppress correlations
+
+        Parameters
+        ----------
+        spacing : int
+            Keep only every 'spacing'th entry of the correlator
+        offset : int
+            Offset the equal spacing
+        """
+        new_content = []
+        for t in range(self.T):
+            if (offset + t) % spacing != 0:
+                new_content.append(None)
+            else:
+                new_content.append(self.content[t])
+        return Corr(new_content)
+
     def correlate(self, partner):
         """Correlate the correlator with another correlator or Obs
 

pyerrors/input/json.py

@@ -171,6 +171,9 @@ def create_json_string(ol, description='', indent=1):
             names.append(key)
             idl.append(value)
         my_obs = Obs(samples, names, idl)
+        my_obs._covobs = obs._covobs
+        for name in obs._covobs:
+            my_obs.names.append(name)
         my_obs.reweighted = obs.reweighted
         my_obs.is_merged = obs.is_merged
         return my_obs

tests/correlators_test.py

@@ -283,3 +283,11 @@ def test_hankel():
     corr.Hankel(2)
     corr.Hankel(6, periodic=True)
 
+
+def test_thin():
+    c = pe.Corr([pe.pseudo_Obs(i, .1, 'test') for i in range(10)])
+    c *= pe.cov_Obs(1., .1, '#ren')
+    thin = c.thin()
+    thin.fit(lambda a, x: a[0] * x)
+    c.thin(offset=1)
+    c.thin(3, offset=1)

tests/json_io_test.py

@@ -244,46 +244,10 @@ def test_json_dict_io():
     os.remove(fname + '.json.gz')
 
 
-def test_openqcd():
-    path = './tests//data/openqcd_test/'
-    prefix = 'sfqcd'
-    postfix = '.rwms'
-
-    # sfqcd-1.6: Trajectories instead of confignumbers are printed to file.
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix)
-    repname = list(rwfo[0].idl.keys())[0]
-    assert(rwfo[0].idl[repname] == range(1, 13))
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[1], r_stop=[12])
-    assert(rwfo[0].idl[repname] == range(1, 13))
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[3], r_stop=[8])
-    assert(rwfo[0].idl[repname] == range(3, 9))
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[2], r_stop=[6])
-    assert(rwfo[0].idl[repname] == range(2, 7))
-    rwfs = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[1], r_stop=[12], r_step=2)
-    assert(rwfs[0].idl[repname] == range(1, 12, 2))
-    rwfs = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[2], r_stop=[12], r_step=2)
-    assert(rwfs[0].idl[repname] == range(2, 13, 2))
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix)
-    assert((rwfo[0].r_values[repname] + rwfo[0].deltas[repname][1]) == (rwfs[0].r_values[repname] + rwfs[0].deltas[repname][0]))
-
-    o = pe.pseudo_Obs(1., .01, repname, samples=12)
-    pe.reweight(rwfo[0], [o])
-
-    o = pe.pseudo_Obs(1., .01, repname, samples=6)
-    pe.reweight(rwfo[0], [o])
-    o.idl[repname] = range(2, 13, 2)
-    pe.reweight(rwfo[0], [o])
-    pe.reweight(rwfs[0], [o])
-
-    files = ['openqcd2r1.ms1.dat']
-    names = ['openqcd2|r1']
-
-    # TM with 2 Hasenbusch factors and 2 sources each + RHMC with one source, openQCD 2.0
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='2.0', files=files, names=names)
-    assert(len(rwfo) == 2)
-    assert(rwfo[0].value == 0.9999974970236312)
-    assert(rwfo[1].value == 1.184681251089919)
-    repname = list(rwfo[0].idl.keys())[0]
-    assert(rwfo[0].idl[repname] == range(1, 10))
-    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='2.0', files=files, names=names, r_start=[1], r_stop=[8])
-    assert(rwfo[0].idl[repname] == range(1, 9))
+def test_renorm_deriv_of_corr(tmp_path):
+    c = pe.Corr([pe.pseudo_Obs(i, .1, 'test') for i in range(10)])
+    c *= pe.cov_Obs(1., .1, '#ren')
+    c = c.deriv()
+    pe.input.json.dump_to_json(c, (tmp_path / 'test').as_posix())
+    recover = pe.input.json.load_json((tmp_path / 'test').as_posix())
+    assert np.all([o == 0 for o in (c - recover)[1:-1]])

tests/openQCD_in_test.py

@@ -0,0 +1,49 @@
+import os
+import numpy as np
+import pyerrors as pe
+import pytest
+
+
+def test_openqcd():
+    path = './tests//data/openqcd_test/'
+    prefix = 'sfqcd'
+    postfix = '.rwms'
+
+    # sfqcd-1.6: Trajectories instead of confignumbers are printed to file.
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix)
+    repname = list(rwfo[0].idl.keys())[0]
+    assert(rwfo[0].idl[repname] == range(1, 13))
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[1], r_stop=[12])
+    assert(rwfo[0].idl[repname] == range(1, 13))
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[3], r_stop=[8])
+    assert(rwfo[0].idl[repname] == range(3, 9))
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[2], r_stop=[6])
+    assert(rwfo[0].idl[repname] == range(2, 7))
+    rwfs = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[1], r_stop=[12], r_step=2)
+    assert(rwfs[0].idl[repname] == range(1, 12, 2))
+    rwfs = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix, r_start=[2], r_stop=[12], r_step=2)
+    assert(rwfs[0].idl[repname] == range(2, 13, 2))
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='1.6', postfix=postfix)
+    assert((rwfo[0].r_values[repname] + rwfo[0].deltas[repname][1]) == (rwfs[0].r_values[repname] + rwfs[0].deltas[repname][0]))
+
+    o = pe.pseudo_Obs(1., .01, repname, samples=12)
+    pe.reweight(rwfo[0], [o])
+
+    o = pe.pseudo_Obs(1., .01, repname, samples=6)
+    pe.reweight(rwfo[0], [o])
+    o.idl[repname] = range(2, 13, 2)
+    pe.reweight(rwfo[0], [o])
+    pe.reweight(rwfs[0], [o])
+
+    files = ['openqcd2r1.ms1.dat']
+    names = ['openqcd2|r1']
+
+    # TM with 2 Hasenbusch factors and 2 sources each + RHMC with one source, openQCD 2.0
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='2.0', files=files, names=names)
+    assert(len(rwfo) == 2)
+    assert(rwfo[0].value == 0.9999974970236312)
+    assert(rwfo[1].value == 1.184681251089919)
+    repname = list(rwfo[0].idl.keys())[0]
+    assert(rwfo[0].idl[repname] == range(1, 10))
+    rwfo = pe.input.openQCD.read_rwms(path, prefix, version='2.0', files=files, names=names, r_start=[1], r_stop=[8])
+    assert(rwfo[0].idl[repname] == range(1, 9))