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(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()