Update the automatic test on the master inside EasyFixModes branch

.github/workflows/python-testsuite.yml

@@ -0,0 +1,53 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ ${{matrix.python-version}} -eq 2.7 ]; then pip install -r requirements2.txt;
+        else pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install
+      run: |
+        sudo apt-get update
+        sudo apt-get install git gfortran libblas-dev liblapack-dev
+        git clone https://github.com/mesonepigreco/CellConstructor.git
+        cd cellconstructor
+        python setup.py install --user
+        cd ..
+
+        python setup.py install --user
+    - name: Test with pytest
+      run: |
+        export OMP_NUM_THREADS=1
+        cd tests
+        # Test excluding very long running tests
+        pytest -v -m "not release"

README.md

@@ -4,6 +4,23 @@ Python implementation of the stochastic self-consistent harmonic approximation (
 This program, when istalled, contains both the python libraries to perform a 
 custom minimization, and manipulate the simulation at your will.
 
+## Why do I need python-sscha?
+
+If you are simulating transport or thermal properties of materials, phase diagrams, or phonon-related properties of materials, than you need python-sscha.
+This is a package that enables you to include the effect of both thermal and quantum phonon fluctuations into your *ab initio* simulations.
+
+The method used by this package is the  Stochastic self-consistent Harmonic Approximation (SSCHA). This is a full-quantum method that optimizes the nuclear wave-function (or density matrix at finite temperature) to minimize the free energy.
+In this way you can simulatie highly anharmonic systems, like those close to a second order phase transition (as charge density waves and thermoelectric materials). 
+Despite the full quantum and thermal nature of the algorithm, the overall computational cost is the comparable to standard classical molecular dynamics. Since the algorithm correctly exploits the symmetries of the crystal, in highly symmetric cases it is also much cheaper. 
+
+python-sscha comes both as a python library that can be runned inside your own workflows and as a stand-alone software, initialized by input scripts with the same syntax as Quantum ESPRESSO.
+
+It can be coupled with any *ab initio* engine for force and energy calculations. It can interact through the Atomic Simulation Environment (ASE), and has an implemented interface for automatic submission of jobs in a remote cluster.
+
+Moreover, it is quite easy to use, a standard input is highly human readable and less than 10 lines!
+So, what are you waiting? Download and install python-sscha, and start enjoing the Tutorials!
+
+
 ## Requirements
 
 The requirements of the python-sscha package are:
@@ -51,8 +68,11 @@ Please, remember that if you use the intel compiler, you need to delete the lapa
 setup.py and include the -mkl (as done for cellconstructor).
 Note that you must force to use the same liker compiler as the one used for the compilation.
 it may be necessary to specify
+
 MPICC=mpiicc LDSHARED="mpiicc -shared" python setup.py install
 
+A specific setup.py script is provided to install it easily in FOSS clusters.
+
 Remember to use the same compiler that you used to compile the pypar library, 
 otherwise when calling MPI_Init() on the initialization, the code will complain and crash.
 
@@ -67,6 +87,8 @@ sscha -i input_file
 Where the "input_file" is a valid input for the code. Please look at the SimpleExample
 inside the Examples directory to see a template and how to create it.
 
+You are strongly encouraged to follow the Tutorials (in the Tutorial directory).
+
 Alternative the code can be used directly as a python library (expert mode).
 This will allow much more customization on the input and the behaviour of the
 code, and the easy interface with calculators different from Quantum ESPRESSO.

Tutorials/SnSe_ToyModel/ffield_dynq1

@@ -0,0 +1,58 @@
+Dynamical matrix file
+
+  2    2  0 12.4000000  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000
+Basis vectors
+     -0.500000000    0.000000000    0.500000000
+      0.000000000    0.500000000    0.500000000
+     -0.500000000    0.500000000    0.000000000
+           1  'Sn  '    108197.545983522     
+           2  'Te  '    116300.285296078     
+    1    2     -0.2500000000     -0.2500000000     -0.2500000000
+    2    1      0.2500000000      0.2500000000      0.2500000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.000000000   0.000000000   0.000000000 ) 
+
+    1    1
+ -0.01395957  0.00000000   -0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.01395957  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000   -0.01395957  0.00000000
+    1    2
+  0.01391577  0.00000000   -0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000    0.01391577  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00000000  0.00000000    0.01391577  0.00000000
+    2    1
+  0.01391577  0.00000000   -0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000    0.01391577  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000    0.01391577  0.00000000
+    2    2
+ -0.01388290  0.00000000   -0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.01388290  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00000000  0.00000000   -0.01388290  0.00000000
+
+
+     Diagonalizing the dynamical matrix
+
+     q = (    0.000000000   0.000000000   0.000000000 ) 
+
+ **************************************************************************
+     freq (    1) =      -1.639295 [THz] =     -54.681001 [cm-1]
+ ( -0.466359  0.000000 -0.457469  0.000000  0.196340  0.000000 ) 
+ (  0.499911  0.000000  0.490382  0.000000 -0.210466  0.000000 ) 
+     freq (    2) =      -1.639295 [THz] =     -54.681001 [cm-1]
+ ( -0.146624  0.000000 -0.130879  0.000000 -0.653215  0.000000 ) 
+ (  0.157173  0.000000  0.140295  0.000000  0.700211  0.000000 ) 
+     freq (    3) =      -1.639295 [THz] =     -54.681001 [cm-1]
+ ( -0.475740  0.000000  0.488785  0.000000  0.008854  0.000000 ) 
+ (  0.509968  0.000000 -0.523951  0.000000 -0.009491  0.000000 ) 
+     freq (    4) =      -0.022835 [THz] =      -0.761710 [cm-1]
+ (  0.223143  0.000000  0.507189  0.000000 -0.437717  0.000000 ) 
+ (  0.223756  0.000000  0.508581  0.000000 -0.438919  0.000000 ) 
+     freq (    5) =      -0.022835 [THz] =      -0.761710 [cm-1]
+ ( -0.390600  0.000000 -0.276341  0.000000 -0.519324  0.000000 ) 
+ ( -0.391672  0.000000 -0.277100  0.000000 -0.520749  0.000000 ) 
+     freq (    6) =      -0.022835 [THz] =      -0.761710 [cm-1]
+ ( -0.544306  0.000000  0.406232  0.000000  0.193226  0.000000 ) 
+ ( -0.545800  0.000000  0.407347  0.000000  0.193756  0.000000 ) 
+ **************************************************************************

Tutorials/SnSe_ToyModel/ffield_dynq2

@@ -0,0 +1,120 @@
+Dynamical matrix file
+
+  2    2  0 12.4000000  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000
+Basis vectors
+     -0.500000000    0.000000000    0.500000000
+      0.000000000    0.500000000    0.500000000
+     -0.500000000    0.500000000    0.000000000
+           1  'Sn  '    108197.545983522     
+           2  'Te  '    116300.285296078     
+    1    2     -0.2500000000     -0.2500000000     -0.2500000000
+    2    1      0.2500000000      0.2500000000      0.2500000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.500000000  -0.500000000   0.500000000 ) 
+
+    1    1
+  0.07290665  0.00000000   -0.00592402  0.00000000    0.00592402  0.00000000
+ -0.00592402  0.00000000    0.07290665  0.00000000   -0.00592402  0.00000000
+  0.00592402  0.00000000   -0.00592402  0.00000000    0.07290665  0.00000000
+    1    2
+  0.00000000  0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000    0.00000000  0.00000000    0.00000000 -0.00000000
+  0.00000000  0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+    2    1
+  0.00000000 -0.00000000   -0.00000000  0.00000000    0.00000000 -0.00000000
+  0.00000000  0.00000000   -0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000    0.00000000  0.00000000    0.00000000 -0.00000000
+    2    2
+  0.05733547  0.00000000   -0.02415651  0.00000000    0.02415651  0.00000000
+ -0.02415651  0.00000000    0.05733547  0.00000000   -0.02415651  0.00000000
+  0.02415651  0.00000000   -0.02415651  0.00000000    0.05733547  0.00000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.500000000   0.500000000  -0.500000000 ) 
+
+    1    1
+  0.07290665  0.00000000    0.00592402  0.00000000   -0.00592402  0.00000000
+  0.00592402  0.00000000    0.07290665  0.00000000   -0.00592402  0.00000000
+ -0.00592402  0.00000000   -0.00592402  0.00000000    0.07290665  0.00000000
+    1    2
+  0.00000000  0.00000000    0.00000000  0.00000000    0.00000000 -0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000    0.00000000 -0.00000000
+  0.00000000 -0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+    2    1
+  0.00000000 -0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000    0.00000000 -0.00000000
+    2    2
+  0.05733547  0.00000000    0.02415651  0.00000000   -0.02415651  0.00000000
+  0.02415651  0.00000000    0.05733547  0.00000000   -0.02415651  0.00000000
+ -0.02415651  0.00000000   -0.02415651  0.00000000    0.05733547  0.00000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (   -0.500000000  -0.500000000  -0.500000000 ) 
+
+    1    1
+  0.07290665  0.00000000    0.00592402  0.00000000    0.00592402  0.00000000
+  0.00592402  0.00000000    0.07290665  0.00000000    0.00592402  0.00000000
+  0.00592402  0.00000000    0.00592402  0.00000000    0.07290665  0.00000000
+    1    2
+ -0.00000000  0.00000000   -0.00000000  0.00000000   -0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00000000  0.00000000   -0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00000000  0.00000000   -0.00000000  0.00000000
+    2    1
+  0.00000000 -0.00000000    0.00000000 -0.00000000    0.00000000 -0.00000000
+  0.00000000 -0.00000000    0.00000000 -0.00000000    0.00000000 -0.00000000
+ -0.00000000 -0.00000000   -0.00000000 -0.00000000   -0.00000000 -0.00000000
+    2    2
+  0.05733547  0.00000000    0.02415651  0.00000000    0.02415651  0.00000000
+  0.02415651  0.00000000    0.05733547  0.00000000    0.02415651  0.00000000
+  0.02415651  0.00000000    0.02415651  0.00000000    0.05733547  0.00000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.500000000  -0.500000000  -0.500000000 ) 
+
+    1    1
+  0.07290665  0.00000000   -0.00592402  0.00000000   -0.00592402  0.00000000
+ -0.00592402  0.00000000    0.07290665  0.00000000    0.00592402  0.00000000
+ -0.00592402  0.00000000    0.00592402  0.00000000    0.07290665  0.00000000
+    1    2
+  0.00000000 -0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00000000 -0.00000000   -0.00000000 -0.00000000
+ -0.00000000  0.00000000   -0.00000000 -0.00000000   -0.00000000 -0.00000000
+    2    1
+  0.00000000  0.00000000    0.00000000 -0.00000000    0.00000000 -0.00000000
+  0.00000000 -0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+    2    2
+  0.05733547  0.00000000   -0.02415651  0.00000000   -0.02415651  0.00000000
+ -0.02415651  0.00000000    0.05733547  0.00000000    0.02415651  0.00000000
+ -0.02415651  0.00000000    0.02415651  0.00000000    0.05733547  0.00000000
+
+     Diagonalizing the dynamical matrix
+
+     q = (    0.500000000  -0.500000000   0.500000000 ) 
+
+ **************************************************************************
+     freq (    1) =       1.821788 [THz] =      60.768295 [cm-1]
+ (  0.000000  0.000000 -0.000000  0.000000  0.000000  0.000000 ) 
+ ( -0.669340  0.000000  0.070285  0.000000  0.739624  0.000000 ) 
+     freq (    2) =       1.821788 [THz] =      60.768295 [cm-1]
+ ( -0.000000  0.000000 -0.000000  0.000000  0.000000  0.000000 ) 
+ (  0.467601  0.000000  0.813466  0.000000  0.345865  0.000000 ) 
+     freq (    3) =       2.496696 [THz] =      83.280831 [cm-1]
+ ( -0.811256  0.000000 -0.485614  0.000000  0.325642  0.000000 ) 
+ ( -0.000000  0.000000 -0.000000  0.000000  0.000000  0.000000 ) 
+     freq (    4) =       2.496696 [THz] =      83.280831 [cm-1]
+ (  0.092359  0.000000 -0.656389  0.000000 -0.748748  0.000000 ) 
+ ( -0.000000  0.000000 -0.000000  0.000000  0.000000  0.000000 ) 
+     freq (    5) =       2.808449 [THz] =      93.679768 [cm-1]
+ ( -0.577350  0.000000  0.577350  0.000000 -0.577350  0.000000 ) 
+ ( -0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 ) 
+     freq (    6) =       3.250858 [THz] =     108.436946 [cm-1]
+ ( -0.000000  0.000000  0.000000  0.000000 -0.000000  0.000000 ) 
+ (  0.577350  0.000000 -0.577350  0.000000  0.577350  0.000000 ) 
+ **************************************************************************

Tutorials/SnSe_ToyModel/ffield_dynq3

@@ -0,0 +1,99 @@
+Dynamical matrix file
+
+  2    2  0 12.4000000  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000
+Basis vectors
+     -0.500000000    0.000000000    0.500000000
+      0.000000000    0.500000000    0.500000000
+     -0.500000000    0.500000000    0.000000000
+           1  'Sn  '    108197.545983522     
+           2  'Te  '    116300.285296078     
+    1    2     -0.2500000000     -0.2500000000     -0.2500000000
+    2    1      0.2500000000      0.2500000000      0.2500000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.000000000  -1.000000000   0.000000000 ) 
+
+    1    1
+  0.01675451  0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.02864983  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000    0.01675451  0.00000000
+    1    2
+ -0.00855040  0.00000000   -0.00000000 -0.00000000   -0.00000000  0.00000000
+  0.00000000 -0.00000000    0.01335965 -0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00000000  0.00000000   -0.00855040  0.00000000
+    2    1
+ -0.00855040 -0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+ -0.00000000 -0.00000000    0.01335965  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000   -0.00855040 -0.00000000
+    2    2
+ -0.00488336  0.00000000   -0.00000000  0.00000000   -0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00193680  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000    0.00000000  0.00000000   -0.00488336  0.00000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (   -1.000000000   0.000000000   0.000000000 ) 
+
+    1    1
+  0.02864983  0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.01675451  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00000000  0.00000000    0.01675451  0.00000000
+    1    2
+  0.01335965 -0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000   -0.00855040  0.00000000    0.00000000 -0.00000000
+  0.00000000 -0.00000000    0.00000000 -0.00000000   -0.00855040  0.00000000
+    2    1
+  0.01335965  0.00000000    0.00000000 -0.00000000   -0.00000000 -0.00000000
+ -0.00000000 -0.00000000   -0.00855040 -0.00000000   -0.00000000 -0.00000000
+  0.00000000  0.00000000   -0.00000000 -0.00000000   -0.00855040 -0.00000000
+    2    2
+ -0.00193680  0.00000000    0.00000000  0.00000000   -0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00488336  0.00000000   -0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00000000  0.00000000   -0.00488336  0.00000000
+
+     Dynamical  Matrix in cartesian axes
+
+     q = (    0.000000000   0.000000000   1.000000000 ) 
+
+    1    1
+  0.01675451  0.00000000    0.00000000  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000    0.01675451  0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00000000  0.00000000    0.02864983  0.00000000
+    1    2
+ -0.00855040 -0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000 -0.00000000   -0.00855040 -0.00000000   -0.00000000 -0.00000000
+  0.00000000  0.00000000   -0.00000000 -0.00000000    0.01335965  0.00000000
+    2    1
+ -0.00855040  0.00000000    0.00000000 -0.00000000    0.00000000  0.00000000
+  0.00000000  0.00000000   -0.00855040  0.00000000    0.00000000 -0.00000000
+  0.00000000  0.00000000    0.00000000 -0.00000000    0.01335965 -0.00000000
+    2    2
+ -0.00488336  0.00000000    0.00000000  0.00000000   -0.00000000  0.00000000
+ -0.00000000  0.00000000   -0.00488336  0.00000000    0.00000000  0.00000000
+ -0.00000000  0.00000000    0.00000000  0.00000000   -0.00193680  0.00000000
+
+     Diagonalizing the dynamical matrix
+
+     q = (    0.000000000  -1.000000000   0.000000000 ) 
+
+ **************************************************************************
+     freq (    1) =      -0.882888 [THz] =     -29.449985 [cm-1]
+ ( -0.311224  0.000000 -0.000000  0.000000 -0.083015  0.000000 ) 
+ ( -0.914722  0.000000  0.000000  0.000000 -0.243990  0.000000 ) 
+     freq (    2) =      -0.882888 [THz] =     -29.449985 [cm-1]
+ ( -0.083015  0.000000  0.000000  0.000000  0.311224  0.000000 ) 
+ ( -0.243990  0.000000 -0.000000  0.000000  0.914722  0.000000 ) 
+     freq (    3) =      -0.830025 [THz] =     -27.686649 [cm-1]
+ ( -0.000000  0.000000  0.347468  0.000000 -0.000000  0.000000 ) 
+ ( -0.000000  0.000000 -0.937692  0.000000 -0.000000  0.000000 ) 
+     freq (    4) =       1.360222 [THz] =      45.372124 [cm-1]
+ (  0.396490  0.000000 -0.000000  0.000000  0.851366  0.000000 ) 
+ ( -0.145004  0.000000 -0.000000  0.000000 -0.311360  0.000000 ) 
+     freq (    5) =       1.360222 [THz] =      45.372124 [cm-1]
+ ( -0.851366  0.000000  0.000000  0.000000  0.396490  0.000000 ) 
+ (  0.311360  0.000000 -0.000000  0.000000 -0.145004  0.000000 ) 
+     freq (    6) =       1.778031 [THz] =      59.308718 [cm-1]
+ ( -0.000000  0.000000 -0.929018  0.000000 -0.000000  0.000000 ) 
+ (  0.000000  0.000000 -0.370034  0.000000  0.000000  0.000000 ) 
+ **************************************************************************