Some scripts used for the phaseD work

scripts/make_runcastep.py

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+#!/usr/bin/env python
+
+_SCRIPT = """#PBS -N castep
+#PBS -l select=5
+#PBS -l walltime=09:00:00
+#PBS -A n03-walk
+#PBS -j oe
+#PBS -m n
+
+# Go to the submit dir - and set environment vars for
+# fortran temp files, OMP etc.
+cd $(readlink -f $PBS_O_WORKDIR)
+export TMPDIR=$(readlink -f $PBS_O_WORKDIR)
+export GFORTRAN_TMPDIR=$(readlink -f $PBS_O_WORKDIR)
+export OMP_NUM_THREADS=1
+
+# Load castep module
+export CASTEP=/usr/local/packages/castep/8.0.0-phase1/bin/castep.mpi
+
+# Run with 120 MPI processes (n), 24 per 24 core node (N),
+# split 12 per NUMA region (S), one thread per MPI process (d)
+# and one hyperthread per core (j). This is 5 nodes
+echo "Starting castep"
+aprun -n 120 -N 24 -S 12 -d 1 -j 1 $CASTEP {basename}
+echo "Castep done"
+"""
+
+def create_runcastep(basename, filename='runcastep.sh'):
+
+    f = open(filename, 'w')
+    f.write(_SCRIPT.format(basename=basename))
+    f.close()
+
+if __name__ == "__main__":
+    import sys
+    import os
+
+    for dir in sys.argv[1:]:
+        file = os.path.join(dir, 'runcastep.sh')
+        create_runcastep(dir, file)
+

scripts/setup_gsf_phaseD.py

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+#!/usr/bin/env python
+
+import numpy as np
+
+from pyDis.atomic import crystal as cry
+from pyDis.atomic import castep_utils as cas
+from pyDis.atomic import atomistic_utils as atm
+from pyDis.pn import  gsf_setup as gsf
+
+path_to_phased = './'
+sc_length = 6 # Number of unit cells along z
+              # must be an even number in this case.
+resolution = 0.33 # Spacing of points in x and y
+
+phaseD = cas.CastepCrystal()
+sys_info = cas.parse_castep('phaseD.cell', phaseD,
+             path=path_to_phased)
+phaseD.translate_cell(0.02*cry.ei(3))
+
+slab = gsf.make_slab(phaseD,sc_length, free_atoms=['Mg', 'O', 'H'])
+atm.scale_kpoints(sys_info['mp_kgrid'],np.array([1,1,sc_length]))
+
+gsf.gamma_surface(slab,resolution,cas.write_castep,sys_info,
+                   basename='gsf_phaseD',suffix='cell', limits=(0.5, 0.5),
+                   mkdir=True)