Fixed some typos and grammatical errors in the documentation.

alm/alamode.cpp

@@ -33,7 +33,7 @@ ALM::ALM(int narg, char **arg)
 {
     std::cout << " +------------------------------------------------------------+" << std::endl;
     std::cout << " +                      Program ALM                           +" << std::endl;
-    std::cout << " +                           Ver. 0.9.4                       +" << std::endl;
+    std::cout << " +                           Ver. 0.9.5                       +" << std::endl;
     std::cout << " +------------------------------------------------------------+" << std::endl;
     std::cout << std::endl;
 

alm/writes.cpp

@@ -389,7 +389,7 @@ void Writes::write_misc_xml()
     ptree pt;
     std::string str_pos[3];
 
-    pt.put("Data.ALM_version", "0.9.4");
+    pt.put("Data.ALM_version", "0.9.5");
     pt.put("Data.Fitting.DisplaceFile", files->file_disp);
     pt.put("Data.Fitting.ForceFile", files->file_force);
     pt.put("Data.Fitting.Constraint", constraint->constraint_mode);

anphon/gruneisen.cpp

@@ -321,7 +321,7 @@ void Gruneisen::write_new_fcsxml(const std::string filename_xml, const double ch
     ptree pt;
     std::string str_pos[3];
 
-    pt.put("Data.ANPHON_version", "0.9.4");
+    pt.put("Data.ANPHON_version", "0.9.5");
     pt.put("Data.Description.OriginalXML", fcs_phonon->file_fcs);
     pt.put("Data.Description.Delta_A", double2string(change_ratio_of_a));
 

anphon/phonons.cpp

@@ -47,7 +47,7 @@ PHON::PHON(int narg, char **arg, MPI_Comm comm)
     if (mympi->my_rank == 0) {
         std::cout << " +------------------------------------------------------------+" << std::endl;
         std::cout << " +                      Program ANPHON                        +" << std::endl;
-        std::cout << " +                           Ver. 0.9.4                       +" << std::endl;
+        std::cout << " +                           Ver. 0.9.5                       +" << std::endl;
         std::cout << " +------------------------------------------------------------+" << std::endl;
 
         std::cout << std::endl;

docs/source/conf.py

@@ -62,7 +62,7 @@
 # The short X.Y version.
 version = '0.9'
 # The full version, including alpha/beta/rc tags.
-release = '0.9.4'
+release = '0.9.5'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/formalism/formalism_anphon.rst

@@ -141,7 +141,7 @@ The one-phonon DOS is given by
 
     \mathrm{DOS}(\omega) = \frac{1}{N_{q}}\sum_{\boldsymbol{q},j}\delta(\omega - \omega_{\boldsymbol{q}j}).
 
-If ``PDOS = 1`` is given, the program also print the atom-projected phonon DOS which is given by
+If ``PDOS = 1`` is given, the program also prints the atom-projected phonon DOS which is given by
 
 .. math::
  
@@ -253,7 +253,7 @@ where :math:`i\omega_{m}` is the Matsubara frequency. In equation :eq:`self3`, w
     e_{\mu}(\kappa;\boldsymbol{q}j)e_{\nu}(\kappa^{\prime};\boldsymbol{q}^{\prime}j^{\prime})e_{\lambda}(\kappa^{\prime\prime};\boldsymbol{q}^{\prime\prime}j^{\prime\prime}) \; ,
     
 
-which becomes zero unless :math:`\boldsymbol{q}+\boldsymbol{q}^{\prime}+\boldsymbol{q}^{\prime\prime}` is a integral multiple of :math:`\boldsymbol{G}=n_{1}\boldsymbol{b}_{1}+n_{2}\boldsymbol{b}_{2}+n_{3}\boldsymbol{b}_{3}`.
+which becomes zero unless :math:`\boldsymbol{q}+\boldsymbol{q}^{\prime}+\boldsymbol{q}^{\prime\prime}` is an integral multiple of :math:`\boldsymbol{G}=n_{1}\boldsymbol{b}_{1}+n_{2}\boldsymbol{b}_{2}+n_{3}\boldsymbol{b}_{3}`.
 Phonon linewidth :math:`\Gamma_{\boldsymbol{q}j}`, which is the imaginary part of the phonon self-energy, can be obtained by the analytic continuation to the real axis (:math:`i\omega_{m}\to \omega + i0^{+}`) as
 
 .. math::
@@ -286,7 +286,7 @@ where :math:`g_{2}` is a dimensionless factor given by
 
     g_{2}(\kappa)=\sum_{i}f_{i}(\kappa)\left(1 - \frac{m_{i}(\kappa)}{M_{\kappa}}\right)^{2}.
 
-Here, :math:`f_{i}` is the fraction of :math:`i`\ th isotope of an element having mass :math:`m_i`, 
+Here, :math:`f_{i}` is the fraction of the :math:`i`\ th isotope of an element having mass :math:`m_i`, 
 and :math:`M_{\kappa}=\sum_{i}f_{i}m_{i}(\kappa)` is the average mass, respectively.
 The :math:`g_{2}` values should be provided by the ``ISOFACT``-tag.
 The average mass :math:`M_{\kappa}` is substituted by the value specified in the ``MASS``-tag.
@@ -333,14 +333,14 @@ When ``ISMEAR = 1``, the delta function is replaced by the Gaussian function as
 which decays faster than the Lorentzian function. 
 For both cases, :math:`\epsilon` should be given by the ``EPSILON``-tag, which must be chosen carefully
 to avoid any unscientific results. :math:`\epsilon` should be small enough to capture detailed phonon structures 
-such as phonon DOS or energy conservation surface related to three-phonon process, but it should be large
-enough to avoid unscientific oscillations. Choosing appropriate value for :math:`\epsilon` is not a trivial task
+such as phonon DOS or energy conservation surface related to three-phonon processes, but it should be large
+enough to avoid unscientific oscillations. Choosing an appropriate value for :math:`\epsilon` is not a trivial task
 since it may depend on the phonon structure and the density of :math:`\boldsymbol{q}` points.
 
 To avoid such issues, the program *anphon* employs the tetrahedron method [5]_ by default (``ISMEAR = -1``)
 for numerical evaluations of Brillouin zone integration containing :math:`\delta(\omega)`.
 When the tetrahedron method is used, the ``EPSILON``-tag is neglected.
-We recommend to use the tetrahedron method whenever possible, even though it may slightly increase the computational cost.
+We recommend using the tetrahedron method whenever possible, even though it may slightly increase the computational cost.
 
 ````
 

docs/source/input/inputalm.rst

@@ -7,7 +7,7 @@ Making input files for *alm*
 Format of input files
 ~~~~~~~~~~~~~~~~~~~~~
 
-Each input file should consists of entry fields.
+Each input file should consist of entry fields.
 Available entry fields are 
 
 **&general**, **&interaction**, **&cutoff**, **&cell**, **&position**, and **&fitting**.
@@ -149,7 +149,7 @@ List of input variables
 +++++++++++++++
 
 In this entry field, one needs to specify cutoff radii of interaction for each order in units of Bohr. 
-In the current implementation, cutoff radii should be defined for every possible pairs of atomic elements. 
+In the current implementation, cutoff radii should be defined for every possible pair of atomic elements. 
 For example, the cutoff entry for a harmonic calculation (``NORDER = 1``) of Si (``NKD = 1``) should be like
 ::
 
@@ -178,8 +178,7 @@ which means that all possible harmonic terms between Si-Si atoms will be include
 
 .. caution::
 
-  Writing None for anharmonic terms can greatly increase the number of parameters, 
-  and hereby increase the computational cost.
+  Writing None for anharmonic terms can greatly increase the number of parameters and thereby increase the computational cost.
 
 When there are more than two atomic elements, please specify the cutoff radii between every possible pairs of atomic elements. In the case of MgO (``NKD = 2``), the cutoff entry should be like
 ::
@@ -300,7 +299,7 @@ This field is necessary when ``MODE = fitting``.
 
  :Default: None
  :Type: String
- :Example: When one wants to consider the rotational invariance around :math:`x`\ -axis, one should give ``ROTAXIS = x``. If one needs additional constraints for the rotation around :math:`y`\ -axis, ``ROTAXIS`` should be ``ROTAXIS = xy``. 
+ :Example: When one wants to consider the rotational invariance around the :math:`x`\ -axis, one should give ``ROTAXIS = x``. If one needs additional constraints for the rotation around the :math:`y`\ -axis, ``ROTAXIS`` should be ``ROTAXIS = xy``. 
 
 ````
 

docs/source/input/inputanphon.rst

@@ -7,7 +7,7 @@ Making input files for *anphon*
 Format of input files
 ~~~~~~~~~~~~~~~~~~~~~
 
-Each input file should consists of entry fields.
+Each input file should consist of entry fields.
 Available entry fields are 
 
 **&general**, **&cell**, **&analysis**, and **&kpoint**.
@@ -243,7 +243,7 @@ The first entry **KPMODE** specifies the types of calculation which is followed
 
 * **KPMODE = 0** : Calculate phonon frequencies at given :math:`k` points
 
- For example, if one wishes to calculate phonon frequencies at Gamma (0, 0, 0) and X (0, 1/2, 1/2) of a FCC crystal, 
+ For example, if one wishes to calculate phonon frequencies at Gamma (0, 0, 0) and X (0, 1/2, 1/2) of an FCC crystal, 
  the ``&kpoint`` entry should be written as
  ::
 
@@ -434,7 +434,7 @@ The first entry **KPMODE** specifies the types of calculation which is followed
  :Default: 0
  :Type: Array of doubles
  :Description: Isotope factor is a dimensionless value defined by :math:`\sum_{i} f_{i} (1 - m_{i}/\bar{m})^{2}`. 
-               Here, :math:`f_{i}` is the fraction of :math:`i`\ th isotope of an element having mass :math:`m_{i}`, 
+               Here, :math:`f_{i}` is the fraction of the :math:`i`\ th isotope of an element having mass :math:`m_{i}`, 
                and :math:`\bar{m}=\sum_{i}f_{i}m_{i}` is the average mass, respectively. 
                This quantity is equivalent to :math:`g_{2}` appearing in the original paper by S. Tamura [Phys. Rev. B, 27, 858.].
 
@@ -479,8 +479,8 @@ Format of BORNINFO
 
 When one wants to consider the LO-TO splitting near the :math:`\Gamma` point, it is necessary to set ``NONANALYTIC = 1`` and
 provide ``BORNINFO`` file containing dielectric tensor :math:`\epsilon^{\infty}` and Born effective charge :math:`Z^{*}`.
-In ``BORNINFO`` file, dielectric tensor should be written in first 3 lines which is followed by Born effective charge tensors
-for each atoms as the following.
+In ``BORNINFO`` file, the dielectric tensor should be written in first 3 lines which are followed by Born effective charge tensors
+for each atom as the following.
 
 .. math::
    :nowrap:

docs/source/install.rst

@@ -29,7 +29,7 @@ Optional requirements
 * Python (> 2.6), Numpy, and Matplotlib
 * XcrySDen_ or VMD_
 
-We provide some small scrips written in Python (Python 2) for visualizing phonon dispersion relations, phonon DOSs, etc.
+We provide some small scripts written in Python (Python 2) for visualizing phonon dispersion relations, phonon DOSs, etc.
 To use these scripts, one need to install the above Python packages.
 Additionally, XcrySDen is necessary to visualize the normal mode directions and animate the normal mode.
 VMD may be more useful to make an animation, but it may be replaced by any other visualization software which support the XYZ format.

docs/source/intro.rst

@@ -67,7 +67,7 @@ If you used ALAMODE, please cite the following article:
 Acknowledgement
 ---------------
 
-This project is support by a Grant-in-Aid for Scientific Research on Innovative Areas 
+This project was supported by a Grant-in-Aid for Scientific Research on Innovative Areas 
 'Materials Design through Computics: Complex Correlation and Non-Equilibrium Dynamics'.
 (http://computics-material.jp)
 
@@ -80,5 +80,5 @@ Author
 
     <script>gen_mail_to_link('Terumasa TADANO', 'terumasa.tadano','gmail.com')</script>
 
-Current affiliation: Department of Physics, The University of Tokyo, Japan
+Current affiliation: Department of Applied Physics, The University of Tokyo, Japan
 

docs/source/quickstart.rst

@@ -48,7 +48,7 @@ Program *alm* estimates harmonic and anharmonic interatomic force constants (IFC
   Then, please prepare necessary input files for a DFT engine (or a classical force field engine) 
   and calculate atomic forces for each displaced configuration.
   Once the atomic forces are calculated for all configurations, please collect the atomic displacements and atomic forces to separate files, say `disp_all.dat` and `force_all.dat`, in Rydberg atomic units. 
-  The details of file format is described in :ref:`this page <label_format_DFILE>`.
+  The detail of the file format is described in :ref:`this page <label_format_DFILE>`.
 
   .. Note::
     We provide some auxiliary Python scripts to expedite the above procedure for VASP and xTAPP users.

docs/source/tutorial.rst

@@ -62,7 +62,7 @@ To do so, you first need to decide the magnitude of displacements :math:`\Delta
 
 Then, prepare input files necessary to run an external DFT code for each configurations.
 Since this procedure is a little tiresome, we provide a subsidiary Python script for VASP, Quantum-ESPRESSO (QE), and xTAPP.
-Using the script :red:`displace.py` in the tools/ directory, you can generate the the necessary input files as follows:
+Using the script :red:`displace.py` in the tools/ directory, you can generate the necessary input files as follows:
 
     **QE**
     ::
@@ -81,7 +81,7 @@ Using the script :red:`displace.py` in the tools/ directory, you can generate th
 
 
 The ``--mag`` option specifies the displacement length in units of Angstrom. 
-You need to specify a input file with equilibrium atomic positions either by the ``--QE``, ``--VASP``, or ``--xTAPP``.
+You need to specify an input file with equilibrium atomic positions either by the ``--QE``, ``--VASP``, or ``--xTAPP``.
 
 Then, calculate atomic forces for all the configurations.
 
@@ -203,7 +203,7 @@ Then, the phonon dispersion is shown by a pop-up window as follows:
 .. image:: ../img/si_phband.png
    :scale: 75
 
-You can save the figure as png, eps, or other format from this window.
+You can save the figure as png, eps, or other formats from this window.
 You can also change the energy unit of phonon frequency from cm\ :sup:`-1` to THz or meV by the ``--unit`` option. 
 For more detail of the usage of :red:`plotband.py`, type
 ::

example/Si/reference/si222.fcs

@@ -1,14 +1,17 @@
  ******************** Force Constants (FCs) ********************
- *     Force constants are printed in Rydberg atomic unit      *
+ *     Force constants are printed in Rydberg atomic units.    *
  *     FC2: Ry/a0^2     FC3: Ry/a0^3     FC4: Ry/a0^4   etc.   *
  *     FC?: Ry/a0^?                                            *
  *     a0= Bohr radius                                         *
+ *                                                             *
+ *     The value shown in the last column is the distance      *
+ *     between the most distant atomic pairs.                  *
  ***************************************************************
 
- ---------------------------------------------------------------
-      Index              FCs         P       Pairs      Distance
- (Global, Local)              (Multiplicity)           (for FC2)
- ---------------------------------------------------------------
+ ----------------------------------------------------------------------
+      Index              FCs         P        Pairs     Distance [Bohr]
+ (Global, Local)              (Multiplicity)                           
+ ----------------------------------------------------------------------
 
   *FC2
        1       1     2.7617453e-01   1     1x     1x       0.000

example/Si/reference/si222.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Data>
-  <ALM_version>0.9.2</ALM_version>
+  <ALM_version>0.9.5</ALM_version>
   <Fitting>
     <DisplaceFile>disp.dat</DisplaceFile>
     <ForceFile>force.dat</ForceFile>