New active learning with AiiDA and FLARE

.github/workflows/python-testsuite.yml

@@ -51,6 +51,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install git gfortran libblas-dev liblapack-dev
+        pip install mir-flare
         git clone https://github.com/SSCHAcode/CellConstructor.git
         pip install meson meson-python ninja
         cd CellConstructor

.gitignore

@@ -65,6 +65,7 @@ frequencies*.*
 timer.json
 minim.dat
 otf_run*
+nohup.out
 disp_*
 _data_tmp_
 

.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.1.0'
+    hooks:
+    -   id: double-quote-string-fixer
+    -   id: end-of-file-fixer
+    -   id: fix-encoding-pragma
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
+        exclude: >-
+            (?x)^(
+                tests/.*.*out|
+                tests/.*.in$
+            )$
+
+-   repo: https://github.com/ikamensh/flynt/
+    rev: '0.76'
+    hooks:
+    -   id: flynt
+
+-   repo: https://github.com/pycqa/isort
+    rev: '5.12.0'
+    hooks:
+    -   id: isort
+
+-   repo: https://github.com/pre-commit/mirrors-yapf
+    rev: 'v0.32.0'
+    hooks:
+    -   id: yapf
+        name: yapf
+        types: [python]
+        args: ['-i']
+        exclude: &exclude_files >
+            (?x)^(
+                docs/.*|
+                tests/.*(?<!\.py)$
+            )$
+        additional_dependencies: ['toml']
+
+-   repo: local
+    hooks:
+    -   id: pylint
+        name: pylint
+        entry: pylint
+        types: [python]
+        language: system
+
+
+-   repo: https://github.com/PyCQA/pydocstyle
+    rev: '6.1.1'
+    hooks:
+    -   id: pydocstyle
+        exclude: *exclude_files
+        additional_dependencies: ['toml']

Examples/sscha_and_aiida/README.md

@@ -1,20 +1,31 @@
 # Instructions
 
-We provide here the script `run_aiida_sscha.py`, which performs a thermal expansion calculation using SSCHA and aiida-quantumespresso. 
+We provide here some scripts to run SSCHA using AiiDA, FLARE machine-learning potential, and a combination of the two as on-the-fly active learning.
 
-It is preferable to execute the example that you already have some experience with both the SSCHA and AiiDA-QuantumEspresso codes. Nevertheless, you can try following the instructions and to run the example.
+* `run_aiida_sscha.py`, which performs a thermal expansion calculation using SSCHA and aiida-quantumespresso. 
+* `run_flare_sscha.py`, which performs a thermal expansion calculation using SSCHA and FLARE machine-learning interatomic potential. 
+* `run_aiida_flare_sscha.py`, which performs an on-the-fly active learning SSCHA calculation using aiida-quantumespresso for DFT and FLARE as the ML potential. 
+
+It is preferable to execute the example that you already have some experience with both the SSCHA and AiiDA-QuantumESPRESSO codes. Nevertheless, you can try following the instructions and to run the example.
 
 ## Installation
 
-We recommend to install all the packages via `mamba` (which is based on top of `conda`). After having installed `mamba`, you can simply run the following:
+We recommend to install all the packages via `mamba` (which is based on `conda`). After having installed `mamba`, you can simply run the following:
 
 ```console
-> mamba create -n aiida-sscha -c conda-forge python gfortran libblas lapack openmpi julia openmpi-mpicc pip numpy scipy spglib aiida-core
-> pip install ase quippy-ase cellconstructor python-sscha aiida-quantumespresso aiida-pseudo
-> mamba activate aiida-sscha
+> mamba create -n sscha-aiida -c conda-forge python gfortran "blas=*=openblas" openblas lapack julia pip numpy scipy spglib pkg-config aiida-core
+> pip install ase cellconstructor python-sscha aiida-quantumespresso aiida-pseudo
+> mamba activate sscha-aiida
 ```
+Then, you should configure an AiiDA profile and the pw.x code in order to use the example script (see also Prerequisites section).
 
-Then, you should configure an AiiDA profile in order to use the example script (see also Prerequisites section).
+For on-the-fly active learning you also need the FLARE package:
+
+```console
+> git clone --depth 1 https://github.com/mir-group/flare.git
+> cd flare
+> pip install .
+```
 
 ## Prerequisites
 
@@ -23,6 +34,7 @@ You need to have installed in the same environment:
 - `cellconstructor`
 - `aiida-core`
 - `aiida-quantumespresso`
+- (optional, for active learning) `mir-flare` 
 
 For the AiiDA part, it is essential the dameon is running and you have:
 1. Configured a computer where to run the code (e.g. on your own laptop; see `aiida-core` docs for further details)
@@ -33,6 +45,8 @@ Please refer to the aiida-core and aiida-quantumespresso for further installatio
 
 ## How-to run 
 
+### SSCHA with the aiida-quantumespresso interface 
+
 Open the `run_aiida_sscha.py` and change the data according to your needs and local installation. Then simply
 
 ```console
@@ -45,4 +59,20 @@ Usually an actual production run would take a while. We suggest to use instead
 > nohup python run_aiida_sscha.py > run_aiida_sscha.log &
 ```
 
+or a submit script at glance.
+
+### On-the-fly active learning SSCHA with aiida-quantumespresso and FLARE interface 
+
+Open the `run_aiida_flare_sscha.py` and change the data according to your needs and local installation. Then simply
+
+```console
+> python run_aiida_flare_sscha.py > run_aiida_sscha.log
+```
+
+Usually an actual production run would take a while. We suggest to use instead
+
+```console
+> nohup python run_aiida_sscha.py > run_aiida_sscha.log &
+```
+
 or a submit script at glance.

Examples/sscha_and_aiida/Si-dynamical-matrix1

@@ -0,0 +1,56 @@
+Dynamical matrix file
+File generated with the CellConstructor by Lorenzo Monacelli
+1 2 0     1.8897259890000000     0.0000000000000000     0.0000000000000000     0.0000000000000000     0.0000000000000000     0.0000000000000000
+Basis vectors
+    2.7154799999999999     2.7154799999999999     0.0000000000000000
+    2.7154799999999999     0.0000000000000000     2.7154799999999999
+    0.0000000000000000     2.7154799999999999     2.7154799999999999
+	1  'Si '  25597.9124185021937592
+    1     1    -0.0000000000000004     0.0000000000000004     0.0000000000000004
+    2     1     1.3577400000000002     1.3577400000000006     1.3577400000000004
+
+     Dynamical Matrix in cartesian axes
+
+     q = (     0.000000000000     0.000000000000     0.000000000000 )
+
+    1    1
+     0.2590944141379855     0.0000000000000000        0.0000000000000001     0.0000000000000000       -0.0000000000000000     0.0000000000000000
+     0.0000000000000001     0.0000000000000000        0.2590944141379854     0.0000000000000000       -0.0000000000000002     0.0000000000000000
+    -0.0000000000000000     0.0000000000000000       -0.0000000000000002     0.0000000000000000        0.2590944141379854     0.0000000000000000
+    1    2
+    -0.2590944141379856     0.0000000000000000       -0.0000000000000000     0.0000000000000000        0.0000000000000000     0.0000000000000000
+    -0.0000000000000001     0.0000000000000000       -0.2590944141379856     0.0000000000000000        0.0000000000000002     0.0000000000000000
+     0.0000000000000001     0.0000000000000000        0.0000000000000002     0.0000000000000000       -0.2590944141379856     0.0000000000000000
+    2    1
+    -0.2590944141379856     0.0000000000000000       -0.0000000000000001     0.0000000000000000        0.0000000000000001     0.0000000000000000
+    -0.0000000000000000     0.0000000000000000       -0.2590944141379856     0.0000000000000000        0.0000000000000002     0.0000000000000000
+     0.0000000000000001     0.0000000000000000        0.0000000000000002     0.0000000000000000       -0.2590944141379855     0.0000000000000000
+    2    2
+     0.2590944141379858     0.0000000000000000        0.0000000000000001     0.0000000000000000       -0.0000000000000001     0.0000000000000000
+     0.0000000000000001     0.0000000000000000        0.2590944141379858     0.0000000000000000       -0.0000000000000001     0.0000000000000000
+    -0.0000000000000001     0.0000000000000000       -0.0000000000000001     0.0000000000000000        0.2590944141379858     0.0000000000000000
+
+     Diagonalizing the dynamical matrix
+
+     q = (     0.000000000000     0.000000000000     0.000000000000 )
+
+***************************************************************************
+   freq (    1) =    -0.00000009 [THz] =    -0.00000305 [cm-1]
+(   0.699099  0.000000  -0.097697  0.000000   0.041428  0.000000 )
+(   0.699099  0.000000  -0.097697  0.000000   0.041428  0.000000 )
+   freq (    2) =     0.00000020 [THz] =     0.00000677 [cm-1]
+(   0.002505  0.000000   0.291167  0.000000   0.644372  0.000000 )
+(   0.002505  0.000000   0.291167  0.000000   0.644372  0.000000 )
+   freq (    3) =     0.00000026 [THz] =     0.00000855 [cm-1]
+(  -0.106088  0.000000  -0.636928  0.000000   0.288216  0.000000 )
+(  -0.106088  0.000000  -0.636928  0.000000   0.288216  0.000000 )
+   freq (    4) =    14.80188490 [THz] =   493.73766382 [cm-1]
+(  -0.042416  0.000000  -0.451763  0.000000  -0.542320  0.000000 )
+(   0.042416  0.000000   0.451763  0.000000   0.542320  0.000000 )
+   freq (    5) =    14.80188490 [THz] =   493.73766382 [cm-1]
+(  -0.515182  0.000000   0.391193  0.000000  -0.285579  0.000000 )
+(   0.515182  0.000000  -0.391193  0.000000   0.285579  0.000000 )
+   freq (    6) =    14.80188490 [THz] =   493.73766382 [cm-1]
+(  -0.482481  0.000000  -0.377992  0.000000   0.352610  0.000000 )
+(   0.482481  0.000000   0.377992  0.000000  -0.352610  0.000000 )
+***************************************************************************

Examples/sscha_and_aiida/Si-dynamical-matrix2

@@ -0,0 +1,98 @@
+Dynamical matrix file
+File generated with the CellConstructor by Lorenzo Monacelli
+1 2 0     1.8897259890000000     0.0000000000000000     0.0000000000000000     0.0000000000000000     0.0000000000000000     0.0000000000000000
+Basis vectors
+    2.7154799999999999     2.7154799999999999     0.0000000000000000
+    2.7154799999999999     0.0000000000000000     2.7154799999999999
+    0.0000000000000000     2.7154799999999999     2.7154799999999999
+	1  'Si '  25597.9124185021937592
+    1     1    -0.0000000000000004     0.0000000000000004     0.0000000000000004
+    2     1     1.3577400000000002     1.3577400000000006     1.3577400000000004
+
+     Dynamical Matrix in cartesian axes
+
+     q = (    -0.184129509332     0.000000000000     0.000000000000 )
+
+    1    1
+     0.3548752551952572     0.0000000000000000        0.0000000000000000     0.0000000000000000       -0.0000000000000000    -0.0000000000000000
+     0.0000000000000000    -0.0000000000000000        0.2477607075541515     0.0000000000000000        0.0000000000000001    -0.0000000000000000
+    -0.0000000000000000     0.0000000000000000        0.0000000000000001     0.0000000000000000        0.2477607075541518     0.0000000000000000
+    1    2
+     0.0000000000000000     0.0000000000000000       -0.0000000000000000     0.0000000000000000        0.0000000000000000    -0.0000000000000000
+     0.0000000000000000     0.0000000000000000        0.0000000000000001     0.0000000000000000       -0.2008555582082014    -0.0000000087796757
+    -0.0000000000000000    -0.0000000000000000       -0.2008555582082012    -0.0000000087796757       -0.0000000000000002    -0.0000000000000000
+    2    1
+     0.0000000000000000    -0.0000000000000000        0.0000000000000000    -0.0000000000000000       -0.0000000000000000     0.0000000000000000
+    -0.0000000000000000    -0.0000000000000000        0.0000000000000001     0.0000000000000000       -0.2008555582082013     0.0000000087796757
+     0.0000000000000000     0.0000000000000000       -0.2008555582082014     0.0000000087796757       -0.0000000000000002     0.0000000000000000
+    2    2
+     0.3548752551952572     0.0000000000000000        0.0000000000000000     0.0000000000000000       -0.0000000000000000    -0.0000000000000000
+     0.0000000000000000    -0.0000000000000000        0.2477607075541515     0.0000000000000000       -0.0000000000000001    -0.0000000000000000
+    -0.0000000000000000     0.0000000000000000       -0.0000000000000001     0.0000000000000000        0.2477607075541518     0.0000000000000000
+
+     Dynamical Matrix in cartesian axes
+
+     q = (     0.000000000000     0.000000000000    -0.184129509332 )
+
+    1    1
+     0.2477607075541515     0.0000000000000000        0.0000000000000000    -0.0000000000000000       -0.0000000000000000     0.0000000000000000
+     0.0000000000000000     0.0000000000000000        0.2477607075541516    -0.0000000000000000        0.0000000000000001    -0.0000000000000000
+    -0.0000000000000000    -0.0000000000000000        0.0000000000000001     0.0000000000000000        0.3548752551952568     0.0000000000000000
+    1    2
+    -0.0000000000000000    -0.0000000000000000       -0.2008555582082013    -0.0000000087796755        0.0000000000000000     0.0000000000000000
+    -0.2008555582082013    -0.0000000087796755       -0.0000000000000002    -0.0000000000000000        0.0000000000000000    -0.0000000000000000
+    -0.0000000000000001    -0.0000000000000000        0.0000000000000000     0.0000000000000000        0.0000000000000001     0.0000000000000000
+    2    1
+    -0.0000000000000000     0.0000000000000000       -0.2008555582082013     0.0000000087796755       -0.0000000000000001     0.0000000000000000
+    -0.2008555582082013     0.0000000087796755       -0.0000000000000002     0.0000000000000000        0.0000000000000000    -0.0000000000000000
+     0.0000000000000000    -0.0000000000000000        0.0000000000000000     0.0000000000000000        0.0000000000000001    -0.0000000000000000
+    2    2
+     0.2477607075541515    -0.0000000000000000        0.0000000000000001    -0.0000000000000000       -0.0000000000000000     0.0000000000000000
+     0.0000000000000001    -0.0000000000000000        0.2477607075541518     0.0000000000000000        0.0000000000000000    -0.0000000000000000
+    -0.0000000000000000    -0.0000000000000000        0.0000000000000000     0.0000000000000000        0.3548752551952572     0.0000000000000000
+
+     Dynamical Matrix in cartesian axes
+
+     q = (     0.000000000000    -0.184129509332     0.000000000000 )
+
+    1    1
+     0.2477607075541516    -0.0000000000000000        0.0000000000000000    -0.0000000000000000        0.0000000000000000    -0.0000000000000000
+     0.0000000000000000     0.0000000000000000        0.3548752551952573    -0.0000000000000000        0.0000000000000001     0.0000000000000000
+     0.0000000000000000     0.0000000000000000        0.0000000000000001    -0.0000000000000000        0.2477607075541516    -0.0000000000000000
+    1    2
+     0.0000000000000000    -0.0000000000000000        0.0000000000000000     0.0000000000000000       -0.2008555582082014    -0.0000000087796755
+    -0.0000000000000000    -0.0000000000000000       -0.0000000000000000    -0.0000000000000000       -0.0000000000000000    -0.0000000000000000
+    -0.2008555582082015    -0.0000000087796755        0.0000000000000001    -0.0000000000000000       -0.0000000000000000    -0.0000000000000000
+    2    1
+     0.0000000000000000     0.0000000000000000       -0.0000000000000000     0.0000000000000000       -0.2008555582082015     0.0000000087796755
+     0.0000000000000000    -0.0000000000000000       -0.0000000000000000     0.0000000000000000        0.0000000000000001     0.0000000000000000
+    -0.2008555582082014     0.0000000087796755       -0.0000000000000000     0.0000000000000000       -0.0000000000000000     0.0000000000000000
+    2    2
+     0.2477607075541516     0.0000000000000000       -0.0000000000000000     0.0000000000000000       -0.0000000000000000     0.0000000000000000
+    -0.0000000000000000    -0.0000000000000000        0.3548752551952571    -0.0000000000000000        0.0000000000000000    -0.0000000000000000
+    -0.0000000000000000    -0.0000000000000000        0.0000000000000000     0.0000000000000000        0.2477607075541518     0.0000000000000000
+
+     Diagonalizing the dynamical matrix
+
+     q = (    -0.184129509332     0.000000000000     0.000000000000 )
+
+***************************************************************************
+   freq (    1) =     4.45331342 [THz] =   148.54652494 [cm-1]
+(  -0.000000  0.000000   0.703431  0.000000   0.072005  0.000000 )
+(   0.000000 -0.000000   0.072005 -0.000000   0.703431 -0.000000 )
+   freq (    2) =     4.45331342 [THz] =   148.54652494 [cm-1]
+(   0.000000 -0.000000  -0.072005 -0.000000   0.703431  0.000000 )
+(  -0.000000  0.000000   0.703431 -0.000000  -0.072005  0.000000 )
+   freq (    3) =    12.24928837 [THz] =   408.59222083 [cm-1]
+(  -0.145074  0.000000   0.000000 -0.000000  -0.000000  0.000000 )
+(  -0.989421  0.000000   0.000000 -0.000000  -0.000000  0.000000 )
+   freq (    4) =    12.24928837 [THz] =   408.59222083 [cm-1]
+(   0.989421  0.000000  -0.000000 -0.000000  -0.000000  0.000000 )
+(  -0.145074  0.000000  -0.000000 -0.000000   0.000000  0.000000 )
+   freq (    5) =    13.77242792 [THz] =   459.39867995 [cm-1]
+(   0.000000 -0.000000   0.411585 -0.000000  -0.574977  0.000000 )
+(   0.000000 -0.000000   0.574977 -0.000000  -0.411585  0.000000 )
+   freq (    6) =    13.77242792 [THz] =   459.39867995 [cm-1]
+(   0.000000 -0.000000   0.574977 -0.000000   0.411585 -0.000000 )
+(   0.000000  0.000000  -0.411585  0.000000  -0.574977  0.000000 )
+***************************************************************************