def make(self, target_dir):
self.get_cell()
self.cell.otherdict.update(self.merge_cell.otherdict)
self.cell.blocks.update(self.merge_cell.blocks)
if self.usp_pot:
pot.add_potentials_usp(self.cell,
self.pot_type,
otfg_patch=self.otfg_patch)
else:
potentials = pot.add_potentials_asc(self.cell, self.xc_functional,
self.rel_pot)
for potential in potentials:
potential.link_files(target_dir)
self.params.xc_functional = self.xc_functional
self.params.cut_off_energy = self.cut_off_energy
if self.efg_only:
self.params.magres_task = "efg"
else:
self.params.magres_task = "nmr"
if self.target_name is None:
self.target_name = self.source_name
cell_target = os.path.join(target_dir, "%s.cell" % self.target_name)
param_target = os.path.join(target_dir, "%s.param" % self.target_name)
sh_target = os.path.join(target_dir, "%s.sh" % self.target_name)
submission_script = SubmissionScript(self.queue, self.num_cores,
self.code, self.target_name)
with open(sh_target, "w+") as sh_target_file,\
open(param_target, "w+") as param_target_file,\
open(cell_target, "w+") as cell_target_file:
print >> sh_target_file, submission_script
print >> param_target_file, self.params
print >> cell_target_file, self.cell
def make(self, target_dir):
self.get_cell()
self.cell.otherdict.update(self.merge_cell.otherdict)
self.cell.blocks.update(self.merge_cell.blocks)
if self.usp_pot:
pot.add_potentials_usp(self.cell, self.pot_type, otfg_patch=self.otfg_patch)
else:
potentials = pot.add_potentials_asc(self.cell, self.xc_functional, self.rel_pot)
for potential in potentials:
potential.link_files(target_dir)
self.params.xc_functional = self.xc_functional
self.params.cut_off_energy = self.cut_off_energy
if self.efg_only:
self.params.magres_task = "efg"
else:
self.params.magres_task = "nmr"
if self.target_name is None:
self.target_name = self.source_name
cell_target = os.path.join(target_dir, "%s.cell" % self.target_name)
param_target = os.path.join(target_dir, "%s.param" % self.target_name)
sh_target = os.path.join(target_dir, "%s.sh" % self.target_name)
submission_script = SubmissionScript(self.queue,
self.num_cores,
self.code,
self.target_name)
with open(sh_target, "w+") as sh_target_file,\
open(param_target, "w+") as param_target_file,\
open(cell_target, "w+") as cell_target_file:
print >>sh_target_file, submission_script
print >>param_target_file, self.params
print >>cell_target_file, self.cell
def make(self, target_dir):
self.get_cell()
self.cell.otherdict.update(self.merge_cell.otherdict)
self.cell.blocks.update(self.merge_cell.blocks)
if self.usp_pot:
pot.add_potentials_usp(self.cell, "kh")
else:
potentials = pot.add_potentials_asc(self.cell, self.xc_functional, True)
for potential in potentials:
potential.link_files(target_dir)
add_constraints(self.cell, self.filter)
self.params.xc_functional = self.xc_functional
self.params.cut_off_energy = self.cut_off_energy
if self.target_name is None:
self.target_name = self.source_name
cell_target = os.path.join(target_dir, "%s.cell" % self.target_name)
param_target = os.path.join(target_dir, "%s.param" % self.target_name)
sh_target = os.path.join(target_dir, "%s.sh" % self.target_name)
submission_script = SubmissionScript(self.queue,
self.num_cores,
self.code,
self.target_name)
with open(sh_target, "w+") as sh_target_file,\
open(param_target, "w+") as param_target_file,\
open(cell_target, "w+") as cell_target_file:
print >>sh_target_file, submission_script
print >>param_target_file, self.params
print >>cell_target_file, self.cell
def make(self, target_dir):
self.get_cell()
self.cell.otherdict.update(self.merge_cell.otherdict)
self.cell.blocks.update(self.merge_cell.blocks)
if self.usp_pot:
pot.add_potentials_usp(self.cell, "kh")
else:
potentials = pot.add_potentials_asc(self.cell, self.xc_functional,
True)
for potential in potentials:
potential.link_files(target_dir)
add_constraints(self.cell, self.filter)
self.params.xc_functional = self.xc_functional
self.params.cut_off_energy = self.cut_off_energy
if self.target_name is None:
self.target_name = self.source_name
cell_target = os.path.join(target_dir, "%s.cell" % self.target_name)
param_target = os.path.join(target_dir, "%s.param" % self.target_name)
sh_target = os.path.join(target_dir, "%s.sh" % self.target_name)
submission_script = SubmissionScript(self.queue, self.num_cores,
self.code, self.target_name)
with open(sh_target, "w+") as sh_target_file,\
open(param_target, "w+") as param_target_file,\
open(cell_target, "w+") as cell_target_file:
print >> sh_target_file, submission_script
print >> param_target_file, self.params
print >> cell_target_file, self.cell
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,
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(self, target_dir):
"""
Write the calculation to the specified target directory.
"""
self.get_cell()
# Get the J-coupling site if we don't have it already
if self.jc_s is None:
self.get_jcoupling_site(target_dir)
# Set up the site in the cell
if self.jc_s is not None:
try:
jc_ion = cell.ions.species(self.jc_s)[self.jc_i-1]
except IndexError:
raise SiteNotPresent("Site {:s} {:d} not present".format(self.jc_s, self.jc_i))
cell.otherdict['jcoupling_site'] = "{:s} {:d}".format(self.jc_s, self.jc_i)
# Remove extraneous kpoints and add in default cell setup
if 'KPOINTS_LIST' in cell.blocks:
del cell.blocks['KPOINTS_LIST']
self.cell.otherdict.update(self.merge_cell.otherdict)
# Sort out .param file
self.params.xc_functional = self.xc_functional
self.params.cut_off_energy = self.cut_off_energy
# Add pseudopotentials
if self.usp_pot:
pot.add_potentials_usp(cell, self.rel_pot)
else:
potentials = pot.add_potentials_asc(cell, self.xc_functional, self.rel_pot)
for potential in potentials:
potential.link_files(target_dir)
# Generate submission script and write all the files out
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)
submission_script = SubmissionScript(self.queue,
self.num_cores,
self.code,
target_name)
sh_target_file = open(sh_target, "w+")
param_target_file = open(param_target, "w+")
cell_target_file = open(cell_target, "w+")
print >>sh_target_file, submission_script
print >>param_target_file, self.params
print >>cell_target_file, cell
sh_target_file.close()
param_target_file.close()
cell_target_file.close()