adding example

parser/parser-phonopy/setup_paths.py

+import sys, os, os.path
+baseDir = os.path.dirname(os.path.abspath(__file__))
+commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
+
+if not commonDir in sys.path:
+    sys.path.insert(0, commonDir)

test/examples/phonon/control.in

+# control file used to get the finite displacements in the phonon calculations
+  xc           pw-lda
+  relativistic atomic_zora scalar
+  k_grid                     12 12 12 
+  # Slightly overconverged kp, would need 10.05
+  sc_accuracy_rho            1E-6
+  sc_accuracy_eev            1E-4
+  sc_accuracy_etot           1E-6
+  sc_accuracy_forces         1E-4
+  sc_iter_limit         100
+
+  occupation_type gaussian  0.01
+
+  mixer           pulay
+    n_max_pulay               10
+    charge_mix_param          0.4
+
+
+  phonon displacement 0.01
+  phonon supercell -1 1 1   1 -1 1  1 1 -1
+  phonon frequency_units cm^-1
+
+#  phonon cv    0     800   801       200
+   phonon dos   0     800   800  1    50
+   phonon free_energy   0  1200  1200 50
+
+
+  phonon band  0     0     0     0.00  0.25  0.25  100   Gamma  Delta
+  phonon band  0.00  0.25  0.25  0     0.5   0.5   100   Delta  X
+  phonon band  0     0.5   0.5   0.25  0.50  0.75  100   X      W
+  phonon band  0.25  0.50  0.75  0.375 0.375 0.75  100   W      K
+  phonon band  0.375 0.375 0.75  0     0     0     100   K      Gamma
+  phonon band  0     0     0     0.25  0.25  0.25  100   Gamma  Lambda
+  phonon band  0.25  0.25  0.25  0.5   0.5   0.5   100   Lambda L
+
+################################################################################
+#
+#  FHI-aims code project
+#  VB, Fritz-Haber Institut, 2009
+#
+#  Suggested "light" defaults for Ge atom (to be pasted into control.in file)
+#  Be sure to double-check any results obtained with these settings for post-processing,
+#  e.g., with the "tight" defaults and larger basis sets.
+#
+################################################################################
+  species        Ge
+#     global species definitions
+    nucleus             32
+    mass                72.64
+#
+    l_hartree           4
+#
+    cut_pot             3.5          1.5  1.0
+    basis_dep_cutoff    1e-4
+#
+    radial_base         54 5.0
+    radial_multiplier   1
+    angular_grids       specified
+      division   0.0947  110
+      division   0.1314  194
+      division   0.7746  302
+#      division   0.8710  434
+#      division   0.9770  590
+#      division   1.1356  770
+#      division   2.6430  974
+#      outer_grid  974
+      outer_grid  302
+################################################################################
+#
+#  Definition of "minimal" basis
+#
+################################################################################
+#     valence basis states
+    valence      4  s   2.
+    valence      4  p   2.
+    valence      3  d  10.
+#     ion occupancy
+    ion_occ      4  s   1.
+    ion_occ      4  p   1.
+    ion_occ      3  d  10.
+################################################################################
+#
+#  Suggested additional basis functions. For production calculations, 
+#  uncomment them one after another (the most important basis functions are
+#  listed first).
+#
+#  Constructed for dimers: 1.80 A, 2.00 A, 2.35 A, 3.00 A, 4.00 A
+#
+################################################################################
+#  "First tier" - improvements: -329.04 meV to -37.61 meV 
+     hydro 2 p 1.4
+     hydro 3 d 4.3
+#     hydro 4 f 7.4
+     hydro 3 s 3.4
+#  "Second tier" - improvements: -13.91 meV to -1.23 meV
+#     hydro 5 g 10.8
+#     hydro 3 d 2.5
+#     hydro 3 p 3.3
+#     hydro 4 f 12
+#     hydro 6 h 15.6
+#     hydro 3 s 7.2
+#  "Third tier" - improvements: -1.47 meV to -0.40 meV
+#     hydro 3 d 5.8
+#     hydro 4 f 4.3
+#     hydro 5 g 11.6
+#     hydro 5 s 14.8
+#     hydro 4 p 3.9
+#  "Fourth tier"  -improvements: -0.39 meV to -0.11 meV
+#     hydro 4 f 23.2
+#     hydro 2 s 6.2
+#     hydro 5 d 9.8
+#     hydro 5 p 6
+#     hydro 6 h 14.8
+#  Further functions - -0.13 meV and below
+#     hydro 5 f 9.6

test/examples/phonon/geometry.in

+lattice_vector 0   2.76360 2.76360
+lattice_vector 2.76360   0 2.76360
+lattice_vector 2.76360 2.76360   0
+atom 0 0 0 Ge 
+atom 1.3818000000 1.3818000000 1.3818000000 Ge

test/examples/phonon/phonopy-FHI-aims-displacement-01/aims.sub

+### run in /bin/bash
+#$ -S /bin/bash
+### join stdout and stderr
+#$ -j y
+### change to current working dir
+#$ -cwd
+### send no mail
+#$ -m n
+### my email address
+#$ -M my
+### Parallel Environment
+#$ -pe impi 16
+### wallclock, e.g. 3600 seconds
+#$ -l h_rt=80000
+### virtual memory (45G is max. on AIMS)
+#$ -l h_vmem=22G
+
+module load impi
+module load mkl
+export LD_LIBRARY_PATH="/afs/@cell/common/soft/intel/Compiler/11.0/c/mkl/lib/em64t/"
+
+
+binary='/u/abha/fhi-aims-13/bin/aims.012513.scalapack.mpi.x'
+
+mpiexec -n $NSLOTS $binary  > tmp.out

test/examples/phonon/phonopy-FHI-aims-displacement-01/aims.sub.po449118

+-catch_rsh /var/spool/SGE6/aims125/active_jobs/449118.1/pe_hostfile /afs/ipp/.cs/intel/impi/4.0.0
+aims125
+aims398
+start_impi_sles11.sh: check for local mpd daemon (1 of 5)
+start_impi_sles11.sh: check for local mpd daemon (2 of 5)
+start_impi_sles11.sh: check for mpd daemons (1 of 5)
+start_impi_sles11.sh: check for mpd daemons (2 of 5)
+start_impi_sles11.sh: got all 2 of 2 nodes
+-catch_rsh /afs/ipp/.cs/intel/impi/4.0.0

test/examples/phonon/phonopy-FHI-aims-displacement-01/control.in

+# control file used to get the finite displacements in the phonon calculations
+  xc           pw-lda
+  relativistic atomic_zora scalar
+  k_grid                     12 12 12 
+  # Slightly overconverged kp, would need 10.05
+  sc_accuracy_rho            1E-6
+  sc_accuracy_eev            1E-4
+  sc_accuracy_etot           1E-6
+  sc_accuracy_forces         1E-4
+  sc_iter_limit         100
+
+  occupation_type gaussian  0.01
+
+  mixer           pulay
+    n_max_pulay               10
+    charge_mix_param          0.4
+
+
+  phonon displacement 0.01
+  phonon supercell -1 1 1   1 -1 1  1 1 -1
+  phonon frequency_units cm^-1
+
+#  phonon cv    0     800   801       200
+   phonon dos   0     800   800  1    50
+   phonon free_energy   0  1200  1200 50
+
+
+  phonon band  0     0     0     0.00  0.25  0.25  100   Gamma  Delta
+  phonon band  0.00  0.25  0.25  0     0.5   0.5   100   Delta  X
+  phonon band  0     0.5   0.5   0.25  0.50  0.75  100   X      W
+  phonon band  0.25  0.50  0.75  0.375 0.375 0.75  100   W      K
+  phonon band  0.375 0.375 0.75  0     0     0     100   K      Gamma
+  phonon band  0     0     0     0.25  0.25  0.25  100   Gamma  Lambda
+  phonon band  0.25  0.25  0.25  0.5   0.5   0.5   100   Lambda L
+
+################################################################################
+#
+#  FHI-aims code project
+#  VB, Fritz-Haber Institut, 2009
+#
+#  Suggested "light" defaults for Ge atom (to be pasted into control.in file)
+#  Be sure to double-check any results obtained with these settings for post-processing,
+#  e.g., with the "tight" defaults and larger basis sets.
+#
+################################################################################
+  species        Ge
+#     global species definitions
+    nucleus             32
+    mass                72.64
+#
+    l_hartree           4
+#
+    cut_pot             3.5          1.5  1.0
+    basis_dep_cutoff    1e-4
+#
+    radial_base         54 5.0
+    radial_multiplier   1
+    angular_grids       specified
+      division   0.0947  110
+      division   0.1314  194
+      division   0.7746  302
+#      division   0.8710  434
+#      division   0.9770  590
+#      division   1.1356  770
+#      division   2.6430  974
+#      outer_grid  974
+      outer_grid  302
+################################################################################
+#
+#  Definition of "minimal" basis
+#
+################################################################################
+#     valence basis states
+    valence      4  s   2.
+    valence      4  p   2.
+    valence      3  d  10.
+#     ion occupancy
+    ion_occ      4  s   1.
+    ion_occ      4  p   1.
+    ion_occ      3  d  10.
+################################################################################
+#
+#  Suggested additional basis functions. For production calculations, 
+#  uncomment them one after another (the most important basis functions are
+#  listed first).
+#
+#  Constructed for dimers: 1.80 A, 2.00 A, 2.35 A, 3.00 A, 4.00 A
+#
+################################################################################
+#  "First tier" - improvements: -329.04 meV to -37.61 meV 
+     hydro 2 p 1.4
+     hydro 3 d 4.3
+#     hydro 4 f 7.4
+     hydro 3 s 3.4
+#  "Second tier" - improvements: -13.91 meV to -1.23 meV
+#     hydro 5 g 10.8
+#     hydro 3 d 2.5
+#     hydro 3 p 3.3
+#     hydro 4 f 12
+#     hydro 6 h 15.6
+#     hydro 3 s 7.2
+#  "Third tier" - improvements: -1.47 meV to -0.40 meV
+#     hydro 3 d 5.8
+#     hydro 4 f 4.3
+#     hydro 5 g 11.6
+#     hydro 5 s 14.8
+#     hydro 4 p 3.9
+#  "Fourth tier"  -improvements: -0.39 meV to -0.11 meV
+#     hydro 4 f 23.2
+#     hydro 2 s 6.2
+#     hydro 5 d 9.8
+#     hydro 5 p 6
+#     hydro 6 h 14.8
+#  Further functions - -0.13 meV and below
+#     hydro 5 f 9.6

test/examples/phonon/phonopy-FHI-aims-displacement-01/geometry.in

+# geometry.in for FHI-aims 
+# | generated by phonopy.FHIaims.write_aims() 
+lattice_vector 5.5271999999999988 0.0000000000000000 0.0000000000000000 
+lattice_vector 0.0000000000000000 5.5271999999999988 0.0000000000000000 
+lattice_vector 0.0000000000000000 0.0000000000000000 5.5271999999999988 
+atom 0.0100000000000000 0.0000000000000000 0.0000000000000000 Ge 
+atom 5.5271999999999988 2.7635999999999994 2.7635999999999994 Ge 
+atom 2.7635999999999994 0.0000000000000000 2.7635999999999994 Ge 
+atom 2.7635999999999989 2.7635999999999994 0.0000000000000000 Ge 
+atom 1.3817999999999995 1.3817999999999997 1.3817999999999997 Ge 
+atom 1.3817999999999993 4.1453999999999986 4.1453999999999986 Ge 
+atom 4.1453999999999986 1.3817999999999997 4.1453999999999986 Ge 
+atom 4.1453999999999986 4.1453999999999986 1.3817999999999997 Ge