Describe changes + other minor tweaks

CHANGES.md

@@ -4,6 +4,7 @@ v1.0.6 (unreleased)
 Functionality Changes
 ---------------------
 
+- Renamed ``cct.vph`` to ``cct.freq`` (in ``qmix.circuit.EmbeddingCircuit``). The normalized photon voltage is equivalent to the normalized frequency. I think frequency is easier to understand so I changed it.
 - Deleted the command line scripts (``bin/``). There was only one script and it was pretty obscure so I descided to delete it.
 - Moved ``qtcurrent_all_freq()`` function from ``qmix.qtcurrent`` to ``qmix.harmonic_balance``. Again, it's a pretty obscure function and it's only used in the ``harmonic_balance`` module, so I moved it.
 - Deleted ``qtcurrent_std`` from ``qmix.qtcurrent``. This function calculated the "standard" output values, but this was pretty arbitrary. It also didn't really simplify the package at all so I deleted it.

CODE_GUIDELINES.md

@@ -74,13 +74,9 @@ Other Notes
 -----------
 
 - For matrix indices, follow this order:
- - frequency (`f`), harmonic (`p`), Bessel function index (`k`), voltage point (`i`)
+ - frequency (`f`), harmonic (`p`), summation index (`k`), voltage point (`i`)
  - e.g., for the Thevenin voltage: `vt[f, p]`
  - e.g., for the Convolution coefficient: `ckh[f, p, k, i]`
 - Use American spelling everywhere to be consistent with the rest of Python.
- - For example:
- - color, not colour (CAN/UK)
- - tunneling, not tunnelling (CAN/UK)
- - meter, not metre (CAN/UK)
  - Note: If you have Aspell installed, you can check your spelling against the American dictionary using: 
  - `aspell -c -d en_US <filename>`

CONTRIBUTING.md

@@ -8,13 +8,13 @@ We welcome contributions via [pull requests](#contributing-new-code). You can al
 Reporting Bugs 
 --------------
 
-If you find any bugs in QMix, please create a new issue through the [GitHub Issue tracker](https://github.com/garrettj403/QMix/issues) with the ``bug`` label. In your message, please include:
- - your operating system,
- - your Python version,
- - your package versions (Numpy, SciPy and Matplotlib), and
- - if applicable, a small code snippet that recreates the error.
+If you find any bugs in QMix, please create a new issue through the [GitHub Issue tracker](https://github.com/garrettj403/QMix/issues) with the ``bug`` label. In your message, please include your:
+ - operating system
+ - Python version
+ - package versions (Numpy, SciPy and Matplotlib)
+ - if applicable, a small code snippet that recreates the error
 
-**Note:** Before reporting a bug, please ensure that you are using the latest version of QMix and that you are using the QMix virtual environment (``QMix/environment-qmix.yaml``).
+**Note:** Before reporting a bug, please ensure that you are using the latest version of QMix and that you are using the QMix virtual environment (``QMix/environment.yml``).
 
 Requesting New Features
 -----------------------
@@ -29,12 +29,8 @@ If you would like to contribute new code to the QMix project, you can fork the r
 Seeking Support
 ---------------
 
-If you are having any problems installing QMix or setting up your simulation, please create a new issue through the [GitHub Issue tracker](https://github.com/garrettj403/QMix/issues) with the ``help wanted`` or ``question`` tag. In your message, please include:
- - your operating system,
- - your Python version, and
- - your package versions (Numpy, SciPy and Matplotlib).
+If you are having any problems installing QMix or setting up your simulation, please create a new issue through the [GitHub Issue tracker](https://github.com/garrettj403/QMix/issues) with the ``help wanted`` or ``question`` tag. In your message, please include your:
+ - operating system
+ - Python version
+ - package versions (Numpy, SciPy and Matplotlib)
 
-Code of Conduct
----------------
-
-If you participate in the QMix project, you must follow our [Code of Conduct](https://github.com/garrettj403/QMix/blob/master/CODE_OF_CONDUCT.md).

README.md

@@ -9,7 +9,7 @@ QMix
 [![Coverage Status](https://coveralls.io/repos/github/garrettj403/QMix/badge.svg?branch=master)](https://coveralls.io/github/garrettj403/QMix?branch=master)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://github.com/garrettj403/QMix/blob/master/LICENSE)
 
-QMix is a software package for simulating the quasiparticle tunneling currents in Superconductor/Insulator/Superconductor (SIS) junctions. In radio astronomy, these junctions are used for heterodyne mixing at millimeter and submillimeter wavelengths. QMix can be used to simulate the behavior of SIS mixers, optimize their performance and investigate experimental results.
+QMix is used to simulate the quasiparticle tunneling currents in Superconductor/Insulator/Superconductor (SIS) junctions. In radio astronomy, these junctions are used for heterodyne mixing at millimeter and submillimeter wavelengths. QMix can be used to simulate the behavior of SIS mixers, optimize their performance and investigate experimental results.
 
 In order to calculate the quasiparticle tunneling currents, QMix uses *multi-tone spectral domain analysis* (see [references](https://garrettj403.github.io/QMix/references.html#references-related-to-multi-tone-spectral-domain-analysis)). Among other applications, this makes QMix ideal for simulating power saturation, higher-order harmonics, sub-harmonic pumping, harmonic mixing and frequency multiplication.
 

environment.yml

@@ -39,6 +39,7 @@ dependencies:
  - gprof2dot
  - memory_profiler
  - line_profiler
+ - pycallgraph
  # for testing
  - pytest>=3.0
  - pip:

qmix/circuit.py

@@ -567,6 +567,16 @@ def unlock(self):
  self.zt.flags.writeable = True
  self.vb.flags.writeable = True
 
+ @property
+ def vph(self):
+ """Get photon voltage.
+
+ For backwards compatibility.
+
+ """
+
+ return self.cct
+
 
 def read_circuit(filename):
  """Build an embedding circuit from an embedding circuit file.