Merge pull request brucefan1983#1389 from tang070205/20260308-phonon

Modify the processing method prior to phonon dispersion calculation

Author: brucefan1983

doc/gpumd/input_files/basis_in.rst

@@ -12,6 +12,5 @@ To run one a simulation using the ``gpumd`` executable, one has to prepare at le
 
    run_in
    model_xyz
-   basis_in
    kpoints_in
    eigenvector_in

doc/gpumd/input_files/index.rst

@@ -13,15 +13,38 @@ File format
 The format of this file must be as follows:
 
 .. code::
+# high symmetry points
+k_points_x(0) k_points_y(0) k_points_z(0) name(0)
+k_points_x(1) k_points_y(1) k_points_z(1) name(1)
+...
 
- N_kpoints
- kx(0) ky(0) kz(0)
- kx(1) ky(1) kz(1)
- ...
- kx(N_kpoints-1) ky(N_kpoints-1) kz(N_kpoints-1)
+
+Example
+-------
+
+For example, the command::
+
+.. code::
+
+ 0 0 0 G
+ 0.5 0 0 M
+ 0.333 0.333 0 K
+ 0 0 0 G
  
-Here,
-* ``N_kpoints`` is the number of k points you want to consider.
-* The remaining lines give the k vectors (in units of 1/Å) you want to consider.
-* The user has to make sure that the k vectors are defined in the reciprocal space with respect to the unit cell chosen.
+or
+
+.. code::
 
+ 0 0 0 G
+ 0.5 0 0.5 X
+ 0.625 0.25 0.625 U
+          #Represents a breakpoint, marking the start of the second path.
+ 0.375 0.375 0.75 K
+ 0 0 0 G
+ 0.5 0.5 0.5 L
+ 0.5 0.25 0.75 W
+ 0.5 0 0.5 X
+
+Here,
+* The first three columns represent the coordinates of high symmetry points. The last column corresponds to names.
+* A blank line indicates a breakpoint or the initiation of a second path.

doc/gpumd/input_files/kpoints_in.rst

@@ -17,19 +17,18 @@ To use this keyword, please make sure the following files have been preprared in
 
    * - Input filename
      - Brief description
-   * - ``basis.in``
-     - Define the mapping from the atom label to the basis label
    * - ``kpoints.in``
-     - Specify the :math:`\boldsymbol{k}`-points
+     - Specify the :math:`\boldsymbol{k}`-points along the high-symmetry paths
+
+
+To use this keyword, :attr:`replicate` keywords must write head in the :attr:`run.in` file.
 
 Syntax
 ------
 
 This keyword is used as follows::
 
-  compute_phonon <cutoff> <displacement>
-
-:attr:`cutoff` is the cutoff distance (in units of Å) for calculating the force constants.
+  compute_phonon <displacement>
 
 :attr:`displacement` is the displacement (in units of Å) for calculating the force constants using the finite-displacement method.
 
@@ -38,13 +37,14 @@ Example
 
 For example, the command::
 
-    compute_phonon 5.0 0.01
+    compute_phonon 0.01
 
-means that one wants to compute the phonon dispersion using a cutoff distance of 5 Å and a displacement of 0.01 Å.
+means that one wants to compute the phonon dispersion using a displacement of 0.01 Å.
 
 Caveats
 -------
 
+
 This keyword should occur after all the :attr:`potential` keywords.
 
 For two-body potentials, the cutoff distance for force constants can be the same as that for force evaluations.

doc/gpumd/input_parameters/compute_phonon.rst

@@ -11,7 +11,7 @@ This file contains the dynamical matrices :math:`D(\boldsymbol{k})` at different
 File format
 -----------
 
-The file contains :attr:`3 * N_basis * N_kpoints` rows and :attr:`6 * N_basis` columns, where :attr:`N_basis` is the number of basis atoms in the unit cell defined in the :ref:`basis.in input file <basis_in>` and :attr:`N_kpoints` is the number of :math:`\boldsymbol{k}`-points in the :ref:`kpoints.in input file <kpoints_in>`.
+The file contains :attr:`3 * N_basis * N_kpoints` rows and :attr:`6 * N_basis` columns, where :attr:`N_basis` is the number of basis atoms in the unit cell defined and :attr:`N_kpoints` is the number of :math:`\boldsymbol{k}`-points from :ref:`kpoints.in input file <kpoints_in>` created.
 
 Each consecutive :attr:`3 * N_basis` rows correspond to one :math:`\boldsymbol{k}`-point.
 For each :math:`\boldsymbol{k}`-point, the first :attr:`3*N_basis` columns correspond to the real part and the second :attr:`3*N_basis` columns correspond to the imaginary part.

doc/gpumd/output_files/D_out.rst

@@ -383,6 +383,7 @@ void Run::parse_one_keyword(std::vector<std::string>& tokens)
     hessian.compute(
       force,
       box,
+      atom.cpu_mass,
       atom.cpu_position_per_atom,
       atom.position_per_atom,
       atom.type,