Merge pull request #84 from MineralsCloud:mpmath

Replace `bigfloat` with `mpmath` in docs

Author: singularitti

README.md

@@ -38,7 +38,7 @@ $ pip install qha
 
 ### Dependencies
 
-- [bigfloat](https://pypi.python.org/pypi/bigfloat)
+- [mpmath](https://mpmath.org/)
 - [lazy-property](https://github.com/jackmaney/lazy-property)
 - [matplotlib](https://matplotlib.org)
 - [Numba](http://numba.pydata.org)
@@ -63,13 +63,6 @@ Notice that you have to use Python version 3.6.x to install. If you want to inst
 $ pip install -e .
 ```
 
-### Trouble shooting of installation
-
-1. Error raised about `mpfr.h` file: To solve this error, `GMP` and `MPFR` libraries are required to use `bigfloat` package.
-   * On Linux, install `libmpfr-dev` , for example, on Ubuntu type `apt-get install libmpfr-dev`;
-   * On Windows, `bigfloat` can be installed from the binary file, please check [“Unofficial Windows Binaries for Python Extension Packages”](https://www.lfd.uci.edu/~gohlke/pythonlibs/), download the version suitable for the system, for example, for a 64-bit system, use pip to install it `pip(3) install /the/path/to/bigfloat‑0.3.0‑cp36‑cp36m‑win_amd64.whl`;
-   * On macOS, install these libraries via `brew install mpfr`. Of course, you need the [Homebrew package manager](https://brew.sh) installed to run this command.
-
 ## Checking the examples
 
 To run the examples, go to `examples/ice VII/` or `examples/silicon/` directories and type in terminal:

docs/source/tutorials/installing.rst

@@ -22,7 +22,7 @@ Our supported platforms are:
 
 Dependencies
 ------------
-- `bigfloat <https://pypi.python.org/pypi/bigfloat>`_ [#b]_
+- `mpmath <https://mpmath.org>`_
 - `lazy-property <https://github.com/jackmaney/lazy-property>`_
 - `matplotlib <https://matplotlib.org>`_ [#m]_
 - `Numba <http://numba.pydata.org>`_
@@ -35,14 +35,6 @@ Dependencies
 
 Notes:
 
-.. [#b] ``GMP`` and ``MPFR`` libraries are required to use ``bigfloat`` package. On macOS,
-    install these libraries via ``brew install mpfr``; on Linux, install ``libmpfr-dev`` ,
-    for example, on Ubuntu use ``apt-get install libmpfr-dev``;
-    on Windows, ``bigfloat`` can be installed from the binary file, please check
-    `Unofficial Windows Binaries for Python Extension Packages <https://www.lfd.uci.edu/~gohlke/pythonlibs/>`_,
-    download the version suitable for the system, for example,for a 64-bit system,
-    use pip to install it ``pip(3) install /the/path/to/bigfloat‑0.3.0‑cp36‑cp36m‑win_amd64.whl``;
-
 .. [#m] For some systems, ``python-tkinter`` package is needed by ``matplotlib``, otherwise the plot function will not work.
 
 Installing the ``qha`` package

qha/multi_configurations/different_phonon_dos.py

@@ -118,11 +118,11 @@ def partition_functions_for_each_configuration(self):
         :return: A matrix, the partition function of each configuration of each volume.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
+        with mpmath.workprec(self.precision):
             # shape = (# of configurations, # of volumes for each configuration)
             exp = np.vectorize(bigfloat.exp)
             return exp(-self.aligned_free_energies_for_each_configuration / (K * self.temperature))
@@ -139,13 +139,13 @@ def partition_functions_for_all_configurations(self):
         :return: A vector, the partition function of each volume.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
+        with mpmath.workprec(self.precision):
             # shape = (# of volumes,)
-            return np.array([bigfloat.exp(d) for d in
+            return np.array([mpmath.exp(d) for d in
                              logsumexp(-self.aligned_free_energies_for_each_configuration.T / (K * self.temperature),
                                        axis=1, b=self.degeneracies)])
 
@@ -160,10 +160,10 @@ def get_free_energies(self):
         :return: The free energy on a temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            log_z = np.array([bigfloat.log(d) for d in self.partition_functions_for_all_configurations], dtype=float)
+        with mpmath.workprec(self.precision):
+            log_z = np.array([mpmath.log(d) for d in self.partition_functions_for_all_configurations], dtype=float)
         return -K * self.temperature * log_z

qha/multi_configurations/same_phonon_dos.py

@@ -84,13 +84,13 @@ def _static_part(self) -> Vector:
         :return: The static contribution on the temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
             raise ImportError(
-                "You need to install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+                "You need to install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            return np.array([bigfloat.exp(d) for d in  # shape = (# of volumes for each configuration, 1)
+        with mpmath.workprec(self.precision):
+            return np.array([mpmath.exp(d) for d in  # shape = (# of volumes for each configuration, 1)
                              logsumexp(-self.static_energies / (K * self.temperature), axis=1, b=self.degeneracies)])
 
     @property
@@ -124,12 +124,12 @@ def get_free_energies(self):
         :return: The free energy on the temperature-volume grid.
         """
         try:
-            import bigfloat
+            import mpmath
         except ImportError:
-            raise ImportError("Install ``bigfloat`` package to use {0} object!".format(self.__class__.__name__))
+            raise ImportError("Install ``mpmath`` package to use {0} object!".format(self.__class__.__name__))
 
-        with bigfloat.precision(self.precision):
-            log_z = np.array([bigfloat.log(d) for d in self.total], dtype=float)
+        with mpmath.workprec(self.precision):
+            log_z = np.array([mpmath.log(d) for d in self.total], dtype=float)
         return -K * self.temperature * log_z
 
 

setup.py

@@ -48,8 +48,8 @@ def find_version(*file_paths):
       install_requires=[
           'lazy_property',
           'numba',
+          'mpmath',
           'numpy',
-          'bigfloat',
           'pandas',
           'scientific-string',
           'scipy',