Develop (qmlcode#38)

* option to calculate only subset of atoms in local representations (qmlcode#26)

* option to calculate only subset of atoms in local representations
* added reference calculation of representations
* finalized reference testing

* fixed error in test

* Atomic kernels memory (qmlcode#27)

* Added local kernels and tests for local kernels

* Slatm (qmlcode#28)

* Updated SLATM, removed ASE, updated docs, updated SLATM tests case

* Added F90 version of get_sbot in SLATM

* Added F2py implementation of get_sbop in slatm

* Fixed remaining issues with f90-slatm, works for global and local now.

* Added testcases for local SLATM

* Removed dead code from slatm.py

* Linear kernel (qmlcode#29)

* Added linear kernel and test

* Updated documentation for kernels and removed compiler warning (from frepresentations)

* Added global ARAD kernel and test

* Linalg (qmlcode#30)

* Added MKL discovery

* Updated cho_solve and cho_invert, so input is conserved

* Added busch-kaufman factorization solver and inversion (DSYTRS)

* Linear kernel (qmlcode#31)

* Added linear kernel and test

* Updated documentation for kernels and removed compiler warning (from frepresentations)

* Added global ARAD and linear global kernel

* Corrected ARAD global kernel to L2 distance

* Bob bug (qmlcode#33)

* Fixed ordering in Bob, added integration test

* Tightened threshold in Bob integration test to 2.8 kcal/mol

* Fchl main (qmlcode#37)

* Added ARAS->FCHL code

* updated fchl kernels code

* Cleaned up FCHL code, parallelized weight ksi functions

* Factor 4 speed in three-body term

* Updated alchemy and speed

* Added global FCHL kernel

* Fixed initialization bug in FCHL global kernel

* Fixed clearing of self-dotprodicts, and removed excessive OMP memory use

* More parallelization issues fixed in FCHL

* Fixed 3-body parallelization, added atomic kernels, added option for no alchemy

* Fixed parallelization memory, added force kernels to FCHL

* Added two- and three-body exponenets as parameters

* Added alchemy module, added custom alchemy vectors.

* Updated parallelization etc.

* Fchl module (qmlcode#34)

* Updated to module and added screening function

* Fixed bug in cut-off function.

* Removed debug output from cut-off function.

* Added FCHL to develop branch

* Updated clang->gcc in macos installation instructions, hattip geoff hutchison

* Updated autodeployment to GH pages and PyPI

Author: andersx

.travis.yml

@@ -1,12 +1,16 @@
 language: python
-
 sudo: required
 dist: trusty
-
 group: edge
-
 deploy:
-  provider: pages
+- provider: pypi
+  user: andersx
+  password:
+    secure: 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
+  on:
+    branch: master
+    condition: ${TRAVIS_PYTHON_VERSION} = "2.7"
+- provider: pages
   local_dir: ${TRAVIS_BUILD_DIR}/docs/build/html
   skip_cleanup: true
   repo: qmlcode/qmlcode.github.io
@@ -15,47 +19,40 @@ deploy:
   on:
     branch: master
     condition: ${TRAVIS_PYTHON_VERSION} = "2.7"
-
 python:
-  - "2.7"
-  - "3.5"
-  - "3.6"
-
+- '2.7'
+- '3.5'
+- '3.6'
 before_install:
-  - sudo apt-get update -qq
-
+- sudo apt-get update -qq
 install:
- - sudo apt-get install -qq gcc gfortran libblas-dev liblapack-dev
- - sudo apt-get install -qq gcc-4.8 gfortran-4.8
- - |
-   if [ ${TRAVIS_PYTHON_VERSION:0:1} = 3 ]; then
-       sudo apt-get install python3-numpy
-       pip3 install scipy
-       python3 setup.py build
-       python3 setup.py install
-       pip3 install sphinx
-       pip3 install sphinx-rtd-theme
-       cd ${TRAVIS_BUILD_DIR}/docs
-       make html
-   elif [ ${TRAVIS_PYTHON_VERSION} = "2.7" ]; then
-       sudo apt-get install python-numpy
-       pip2 install scipy
-       python2 setup.py build
-       python2 setup.py install
-       pip2 install sphinx
-       pip2 install sphinx-rtd-theme
-       cd ${TRAVIS_BUILD_DIR}/docs
-       make html
-   else
-       echo "ERROR: Unknown Python version."
-   fi
-
-
+- sudo apt-get install -qq gcc gfortran libblas-dev liblapack-dev
+- sudo apt-get install -qq gcc-4.8 gfortran-4.8
+- |
+  if [ ${TRAVIS_PYTHON_VERSION:0:1} = 3 ]; then
+      sudo apt-get install python3-numpy
+      pip3 install scipy
+      python3 setup.py build
+      python3 setup.py install
+      pip3 install sphinx
+      pip3 install sphinx-rtd-theme
+      cd ${TRAVIS_BUILD_DIR}/docs
+      make html
+  elif [ ${TRAVIS_PYTHON_VERSION} = "2.7" ]; then
+      sudo apt-get install python-numpy
+      pip2 install scipy
+      python2 setup.py build
+      python2 setup.py install
+      pip2 install sphinx
+      pip2 install sphinx-rtd-theme
+      cd ${TRAVIS_BUILD_DIR}/docs
+      make html
+  else
+      echo "ERROR: Unknown Python version."
+  fi
 before_script:
- - cd ${TRAVIS_BUILD_DIR}/tests/
-
+- cd ${TRAVIS_BUILD_DIR}/tests/
 script:
- - nosetests -v
-
+- nosetests -v
 notifications:
   email: false

docs/source/examples.rst

@@ -1,4 +1,4 @@
-Examples
+xamples
 --------
 
 Generating representations using the ``Compound`` class
@@ -106,19 +106,25 @@ The easiest way to calculate the kernel matrix using an explicit, local represen
 .. code:: python
 
     import numpy as np
-    from qml.wrappers import get_atomic_kernels_gaussian
+    from qml.kernels import get_local_kernels_gaussian
 
     # Assume the QM7 dataset is loaded into a list of Compound()
     for compound in qm7:
 
         # Generate the desired representation for each compound
         compound.generate_atomic_coulomb_matrix(size=23, sort="row-norm")
 
+    # Make a big array with all the atomic representations
+    X = np.concatenate([mol.representation for mol in qm7])
+
+    # Make an array with the number of atoms in each compound
+    N = np.array([mol.natoms for mol in qm7])
+
     # List of kernel-widths
     sigmas = [50.0, 100.0, 200.0]
 
     # Calculate the kernel-matrix
-    K = get_atomic_kernels_gaussian(qm7, qm7, sigmas)
+    K = get_local_kernels_gaussian(X, X, N, N, sigmas)
 
     print(K.shape)
 

docs/source/installation.rst

@@ -70,8 +70,7 @@ using ``brew``:
     # Install GCC
     brew install gcc
 
-Note the Clang Fortran compiler from brew unfortunately does not support
-OpenMP.
+Note the Fortran compiler from brew (gfortran) unfortunately does not support OpenMP.
 Therefore parallelism via OpenMP is disabled as default for MacOS systems.
 
 Additionally, we found that some users have multiple version of the ``as`` assembler - this might happen if you have GCC from e.g. brew and macports at the same time. Look for the following error:

docs/source/qml.rst

@@ -52,6 +52,13 @@ qml\.arad module
     :members:
     :show-inheritance:
 
+qml\.fchl module
+----------------
+
+.. automodule:: qml.fchl
+    :members:
+    :show-inheritance:
+
 
 qml\.wrappers module
 --------------------

mkldiscover.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+# MIT License
+#
+# Copyright (c) 2017 Anders Steen Christensen
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from __future__ import print_function
+
+import os
+
+def mkl_exists(verbose=False):
+
+    # Get environment variables
+    __MKLROOT__ = os.environ.get('MKLROOT')
+    __LD_LIBRARY_PATH__ = os.environ.get('LD_LIBRARY_PATH')
+
+    # Check if $MKLROOT is set
+
+    if __MKLROOT__ is None:
+
+        if verbose: 
+            print("MKL-discover: MKLROOT was not set")
+
+        return False
+
+    else:
+
+        if verbose: 
+            print("MKL-discover: MKLROOT was set to")
+            print(__MKLROOT__)
+
+    # Check if path exists
+    mklroot_exists = os.path.isdir(__MKLROOT__)
+    
+    if not mklroot_exists:
+        if verbose: 
+            print("MKL-discover: MKLROOT path does not exist")
+
+        return False
+
+    found_libmkl_rt = False
+
+    # Check if libmkl_rt.so exists below $MKLROOT
+    for dirpath, dirnames, filenames in os.walk(__MKLROOT__, followlinks=True):
+
+        if "libmkl_rt.so" in filenames:
+
+            if verbose:
+                print("MKL-discover: Found libmkl_rt.so at ", dirpath)
+
+            # Check that the dirpath where libmkl_rt.so is in $LD_LIBRARY_PATH
+            if dirpath in __LD_LIBRARY_PATH__:
+
+                if verbose:
+                    print("MKL-discover: Found %s in $LD_LIBRARY_PATH" % dirpath)
+                    print("MKL-discover: Concluding that MKL can be used.")
+                found_libmkl_rt = True
+
+
+    return found_libmkl_rt
+
+if __name__ == "__main__":
+
+    mkl_present = mkl_exists(verbose=False)
+
+    if mkl_present:
+        print("MKL could be found")
+    else:
+        print("MKL could NOT be found")