print >>script, "qsub %s.sh" % name
print >>script, "cd .."
os.chmod(script_path, 0755)
def make_magres_accum_script(root_dir, root_name, runs):
script_path = os.path.join(root_dir, "magres_accum.sh")
script = open(script_path, "w+")
for target_dir, name in runs:
print >>script, "grep isc %s/%s.magres >> %s-isc.magres" % (target_dir, name, root_name)
os.chmod(script_path, 0755)
if __name__ == "__main__":
source_dir, name = calc_from_path(sys.argv[1])
target_dir_prefix = sys.argv[2]
s = sys.argv[3]
i = int(sys.argv[4])
if not os.path.isdir(target_dir_prefix):
os.mkdir(target_dir_prefix)
runs = []
for x in [float(xp)/100.0 for xp in range(0,10)]:
run_dir = "%s-%f" % (name, x)
target_dir = os.path.join(target_dir_prefix, run_dir)
if not os.path.isdir(target_dir):
os.mkdir(target_dir)
from castepy import calc
from castepy.util import calc_from_path, path
relax_path = path("templates/spectral")
merge_cell = cell.Cell(open(os.path.join(relax_path, "spectral.cell")).read())
def make(source_dir, source_name, target_dir):
cal = calc.CastepCalc(source_dir, source_name)
c = cell.Cell(cal.cell_file)
c.other += merge_cell.other
target_cell = os.path.join(target_dir, "%s.cell" % source_name)
target_param = os.path.join(target_dir, "%s.param" % source_name)
target_sh = os.path.join(target_dir, "%s.sh" % source_name)
shutil.copyfile(os.path.join(relax_path, "spectral.param"), target_param)
shutil.copyfile(os.path.join(relax_path, "spectral.sh"), target_sh)
cell_out = open(target_cell, "w+")
print >>cell_out, str(c)
if __name__ == "__main__":
source_calc = str(sys.argv[1])
source_dir, source_name = calc_from_path(source_calc)
target_dir = str(sys.argv[2])
make(source_dir, source_name, target_dir)
for target_dir, name in runs:
print >> script, "grep efg %s/%s.magres >> %s-isc.magres" % (
target_dir, name, root_name)
os.chmod(script_path, 0755)
if __name__ == "__main__":
task_name = sys.argv[1]
source_dir = sys.argv[2]
target_dir_prefix = sys.argv[3]
if not os.path.isdir(target_dir_prefix):
os.mkdir(target_dir_prefix)
runs = []
for cell_path in [x for x in os.listdir(source_dir) if ".cell" in x]:
dir, name = calc_from_path(cell_path)
run_dir = name
target_dir = os.path.join(target_dir_prefix, run_dir)
if not os.path.isdir(target_dir):
os.mkdir(target_dir)
task.make_task(task_name, source_dir, name, target_dir)
runs.append((run_dir, name))
make_submit_all_script(target_dir_prefix, runs)
#make_magres_accum_script(target_dir_prefix, name, runs)
for target_dir, name in runs:
print >>script, "grep efg %s/%s.magres >> %s-isc.magres" % (target_dir, name, root_name)
os.chmod(script_path, 0755)
if __name__ == "__main__":
task_name = sys.argv[1]
source_dir = sys.argv[2]
target_dir_prefix = sys.argv[3]
if not os.path.isdir(target_dir_prefix):
os.mkdir(target_dir_prefix)
runs = []
for cell_path in [x for x in os.listdir(source_dir) if ".cell" in x]:
dir, name = calc_from_path(cell_path)
run_dir = name
target_dir = os.path.join(target_dir_prefix, run_dir)
if not os.path.isdir(target_dir):
os.mkdir(target_dir)
task.make_task(task_name, source_dir, name, target_dir)
runs.append((run_dir, name))
make_submit_all_script(target_dir_prefix, runs)
#make_magres_accum_script(target_dir_prefix, name, runs)
def make(source,
target_dir,
target_name=None,
num_cores=32,
queue="parallel.q",
xc_functional="pbe",
cut_off_energy=50,
ncp_pot=False,
rel_pot=False,
efg=False,
c=None,
**kwargs):
source_dir, source_name = calc_from_path(source)
calc = CastepCalc(source_dir, source_name)
xc_functional = xc_functional.lower()
if c is None:
c = cell.Cell(calc.cell_file)
c.other += merge_cell.other
c.blocks.update(merge_cell.blocks)
if ncp_pot:
if xc_functional == 'pbe':
_, required_files = pot.add_potentials(settings.NCP_PSPOT_PBE_DIR,
None, c, rel_pot)
elif xc_functional == 'lda':
_, required_files = pot.add_potentials(settings.NCP_PSPOT_LDA_DIR,
None, c, rel_pot)
else:
raise Exception("Cannot use XC functional %s with NCPs" %
xc_functional)
pot.link_files(required_files, target_dir)
else:
print rel_pot
pot.add_potentials_usp(c, rel_pot)
if target_name is None:
target_name = source_name
cell_target = os.path.join(target_dir, "%s.cell" % target_name)
param_target = os.path.join(target_dir, "%s.param" % target_name)
sh_target = os.path.join(target_dir, "%s.sh" % target_name)
sh_context = {
'seedname': target_name,
'num_cores': num_cores,
'h_vmem': float(num_cores) / 8 * 23,
'queue': queue,
'CASTEPY_ROOT': settings.CASTEPY_ROOT,
'USER_EMAIL': settings.USER_EMAIL,
}
sh_source = open(os.path.join(nmr_path, "nmr.sh")).read()
sh_target_file = open(sh_target, "w+")
param_target_file = open(param_target, "w+")
params.xc_functional[0] = xc_functional
params.cut_off_energy[0] = cut_off_energy
if efg:
params.magres_task = "efg"
else:
params.magres_task = "nmr"
print >> sh_target_file, sh_source % sh_context
print >> param_target_file, params
cell_out = open(cell_target, "w+")
print >> cell_out, c
sh_target_file.close()
def make(source_dir, source_name, target_dir):
calc = CastepCalc(source_dir, source_name)
target_cell = os.path.join(target_dir, "%s.cell" % source_name)
target_param = os.path.join(target_dir, "%s.param" % source_name)
target_sh = os.path.join(target_dir, "%s.sh" % source_name)
shutil.copyfile(os.path.join(source_dir, "%s.sh" % source_name), target_sh)
# Find .DAT files for J-coupling to link, maybe redo this so it uses pot.linkfiles
for f in os.listdir(source_dir):
if '.DAT' in f:
source = os.path.abspath(os.path.join(source_dir, f))
target = os.path.join(target_dir, f)
if not os.path.isfile(target):
os.symlink(source, target)
cell_out = open(target_cell, "w+")
print >>cell_out, calc.cell_file
param_out = open(target_param, "w+")
print >>param_out, calc.param_file
if __name__ == "__main__":
source_calc = str(sys.argv[1])
dir, name = calc_from_path(source_calc)
target_dir = str(sys.argv[2])
make(dir, name, target_dir)
def make(source_dir, source_name, target_dir, relax_species=["H"]):
calc = calc.CastepCalc(source_dir, source_name)
calc.load(include=['cell', 'param'])
if relax_species is None:
filter = lambda ion: False
else:
filter = lambda ion: ion.s not in relax_species
#c.other += merge_cell.other
target_cell = os.path.join(target_dir, "%s.cell" % source_name)
target_param = os.path.join(target_dir, "%s.param" % source_name)
target_sh = os.path.join(target_dir, "%s.sh" % source_name)
shutil.copyfile(os.path.join(relax_path, "relax.param"), target_param)
shutil.copyfile(os.path.join(relax_path, "relax.sh"), target_sh)
cell_out = open(target_cell, "w+")
print >> cell_out, str(c)
if __name__ == "__main__":
source_calc = str(sys.argv[1])
source_dir, source_name = calc_from_path(source_calc)
target_dir = str(sys.argv[2])
make(source_dir, source_name, target_dir)
def make(
source,
target_dir,
target_name=None,
num_cores=32,
queue="parallel.q",
xc_functional="pbe",
cut_off_energy=50,
ncp_pot=False,
rel_pot=False,
efg=False,
c=None,
**kwargs
):
source_dir, source_name = calc_from_path(source)
calc = CastepCalc(source_dir, source_name)
xc_functional = xc_functional.lower()
if c is None:
c = cell.Cell(calc.cell_file)
c.other += merge_cell.other
c.blocks.update(merge_cell.blocks)
if ncp_pot:
if xc_functional == "pbe":
_, required_files = pot.add_potentials(settings.NCP_PSPOT_PBE_DIR, None, c, rel_pot)
elif xc_functional == "lda":
_, required_files = pot.add_potentials(settings.NCP_PSPOT_LDA_DIR, None, c, rel_pot)
else:
raise Exception("Cannot use XC functional %s with NCPs" % xc_functional)
pot.link_files(required_files, target_dir)
else:
print rel_pot
pot.add_potentials_usp(c, rel_pot)
if target_name is None:
target_name = source_name
cell_target = os.path.join(target_dir, "%s.cell" % target_name)
param_target = os.path.join(target_dir, "%s.param" % target_name)
sh_target = os.path.join(target_dir, "%s.sh" % target_name)
sh_context = {
"seedname": target_name,
"num_cores": num_cores,
"h_vmem": float(num_cores) / 8 * 23,
"queue": queue,
"CASTEPY_ROOT": settings.CASTEPY_ROOT,
"USER_EMAIL": settings.USER_EMAIL,
}
sh_source = open(os.path.join(nmr_path, "nmr.sh")).read()
sh_target_file = open(sh_target, "w+")
param_target_file = open(param_target, "w+")
params.xc_functional[0] = xc_functional
params.cut_off_energy[0] = cut_off_energy
if efg:
params.magres_task = "efg"
else:
params.magres_task = "nmr"
print >> sh_target_file, sh_source % sh_context
print >> param_target_file, params
cell_out = open(cell_target, "w+")
print >> cell_out, c
sh_target_file.close()
