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Added documentation for the PERIODIC tag.
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ttadano committed Jun 27, 2015
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24 changes: 20 additions & 4 deletions docs/source/input/inputalm.rst
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Expand Up @@ -125,6 +125,22 @@ List of input variables

````

* PERIODIC-tag = PERIODIC[1], PERIODIC[2], PERIODIC[3]

===== ====================================================
0 | Do not consider periodic boundary conditions when
| searching for interacting atoms.

1 | Consider periodic boundary conditions when
| searching for interacting atoms.
===== ====================================================

:Default: 1 1 1
:type: Array of integers
:Description: This tag is useful for generating interacting atoms in low dimensional systems. When ``PERIODIC[i]`` is zero, periodic boundary condition is turned off along the direction of the lattice vector :math:`\boldsymbol{a}_{i}`.

````

"&interaction"-field
++++++++++++++++++++

Expand All @@ -141,7 +157,7 @@ List of input variables

:Default: ``NBODY`` = [2, 3, 4, ..., ``NORDER`` + 1]
:Type: Array of integers
:Example: If one wishes to exclude three-body interactions from cubic force constants, one should explicitly give ``NBODY = 2 2``.
:Example: If one wants to exclude three-body interactions from cubic force constants, one should explicitly give ``NBODY = 2 2``.

````

Expand All @@ -161,7 +177,7 @@ This means that the cutoff radii of 10 :math:`a_{0}` will be used for harmonic S
Please note that the first column should be two character strings, which are contained in the ``KD``-tag,
connected by a hyphen (’-’).

When one wishes to consider cubic terms (``NORDER = 2``), please specify the cutoff radius for cubic terms in the third column as the following::
When one wants to consider cubic terms (``NORDER = 2``), please specify the cutoff radius for cubic terms in the third column as the following::

&cutoff
Expand All @@ -178,7 +194,7 @@ 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 thereby increase the computational cost.
Setting '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
::
Expand Down Expand Up @@ -274,7 +290,7 @@ This field is necessary when ``MODE = fitting``.

:Default: ``NSTART = 1``, ``NEND = NDATA``
:Type: Integer
:Example: When one wishes to use the data in the range of [20:30] out of 50 entries, one should set ``NSTART = 20`` and ``NEND = 30``.
:Example: To use the data in the range of [20:30] out of 50 entries, the tags should be ``NSTART = 20`` and ``NEND = 30``.

````

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4 changes: 2 additions & 2 deletions docs/source/input/inputanphon.rst
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Expand Up @@ -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 an FCC crystal,
For example, if one wants 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
::

Expand All @@ -255,7 +255,7 @@ The first entry **KPMODE** specifies the types of calculation which is followed

* **KPMODE = 1** : Band dispersion calculation

For example, if one wishes to calculate phonon dispersion relations along G\-K\-X\-G\-L of a FCC crystal,
For example, if one wants to calculate phonon dispersion relations along G\-K\-X\-G\-L of a FCC crystal,
the ``&kpoint`` entry should be written as follows::

&kpoint
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4 changes: 2 additions & 2 deletions docs/source/quickstart.rst
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Expand Up @@ -77,9 +77,9 @@ Program anphon

To perform phonon calculations and thermal conductivity calculations, one needs to prepare another input file, say `anphon.in`, for the program *anphon*.

If one wishes to perform (harmonic) phonon calculations, one should write ``MODE = phonons`` in the ``&general`` entry of anphon.in. Please make sure that ``FCSXML`` variable being set to the XML file generated by *alm*.
If one wants to perform (harmonic) phonon calculations, one should write ``MODE = phonons`` in the ``&general`` entry of anphon.in. Please make sure that ``FCSXML`` variable being set to the XML file generated by *alm*.

If one wishes to perform thermal conductivity calculations instead of usual phonon calculations, please switch to ``MODE = RTA`` with appropriate ``FCSXML`` containing cubic IFCs.
If one wants to conduct thermal conductivity calculations instead of usual phonon calculations, please switch to ``MODE = RTA`` with appropriate ``FCSXML`` containing cubic IFCs.

For details of input variables of anphon, please refer to the :ref:`list of input variables for anphon <label_inputvar_anphon>`.

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