From f3d5323155a4573292059506c48028d1dfa0643c Mon Sep 17 00:00:00 2001
From: Andrew Walker <a.walker@leeds.ac.uk>
Date: Thu, 4 Feb 2016 10:22:33 +0000
Subject: [PATCH 1/3] For now, stick my phaseD GSF setup script in here.

---
 scripts/setup_gsf_phaseD.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100755 scripts/setup_gsf_phaseD.py

diff --git a/scripts/setup_gsf_phaseD.py b/scripts/setup_gsf_phaseD.py
new file mode 100755
index 0000000..1d3bf3c
--- /dev/null
+++ b/scripts/setup_gsf_phaseD.py
@@ -0,0 +1,25 @@
+#!/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.
+spacing = (8, 8) # Number of points in a and b
+
+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,spacing,cas.write_castep,sys_info,
+                   basename='gsf_phaseD',suffix='cell', limits=(0.5, 0.5),
+                   mkdir=True)

From e53eeb49d8df66e7b29606bec432b924e43075db Mon Sep 17 00:00:00 2001
From: Andrew Walker <a.walker@leeds.ac.uk>
Date: Wed, 9 Mar 2016 09:23:49 +0000
Subject: [PATCH 2/3] Simple tool to write queue manager files for ARCHER

I don't think we will want to distribute this, but I'm
sticking it here for safe keeping.
---
 scripts/make_runcastep.py | 41 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100755 scripts/make_runcastep.py

diff --git a/scripts/make_runcastep.py b/scripts/make_runcastep.py
new file mode 100755
index 0000000..9b7581f
--- /dev/null
+++ b/scripts/make_runcastep.py
@@ -0,0 +1,41 @@
+#!/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)
+

From b979bc7c72995be96ef722f3760992b4c6aa7b50 Mon Sep 17 00:00:00 2001
From: Andrew Walker <a.walker@leeds.ac.uk>
Date: Wed, 9 Mar 2016 11:56:46 +0000
Subject: [PATCH 3/3] Update setup_gsf_phaseD.py to work with current
 gsf_setup.py

---
 scripts/setup_gsf_phaseD.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/setup_gsf_phaseD.py b/scripts/setup_gsf_phaseD.py
index 1d3bf3c..0c15fac 100755
--- a/scripts/setup_gsf_phaseD.py
+++ b/scripts/setup_gsf_phaseD.py
@@ -10,7 +10,7 @@
 path_to_phased = './'
 sc_length = 6 # Number of unit cells along z
               # must be an even number in this case.
-spacing = (8, 8) # Number of points in a and b
+resolution = 0.33 # Spacing of points in x and y
 
 phaseD = cas.CastepCrystal()
 sys_info = cas.parse_castep('phaseD.cell', phaseD,
@@ -20,6 +20,6 @@
 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,spacing,cas.write_castep,sys_info,
+gsf.gamma_surface(slab,resolution,cas.write_castep,sys_info,
                    basename='gsf_phaseD',suffix='cell', limits=(0.5, 0.5),
                    mkdir=True)