def test_to_string(self):
"""
Does generating a .cell file from the object work and is it consistent?
"""
c1 = cell.Cell(open(self.cell1_path).read())
c2 = cell.Cell(str(c1))
self.assertEqual(str(c1), str(c2))
def test_lattice_abc(self):
c = cell.Cell(open(self.cell2_path).read())
lattice = [[6.0, 0.0, 0.0], [0.0, 6.0, 0.0], [0.0, 0.0, 6.0]]
self.assertTrue(
numpy.allclose(c.lattice, lattice, rtol=1e-05, atol=1e-08))
def test_al(self):
"""
Read in ethanol cell and check contents.
"""
for f in os.listdir(self.cells_path):
print f
path = os.path.join(self.cells_path, f)
try:
c = cell.Cell(open(path).read())
except Exception, e:
print type(e), e
def test_ethanol(self):
"""
Read in ethanol cell and check contents.
"""
c = cell.Cell(open(self.cell1_path).read())
self.assertEqual(c.ions_type, 'POSITIONS_ABS')
self.assertEqual(c.ions_units, 'ang')
self.assertEqual(c.lattice_type, 'LATTICE_CART')
self.assertEqual(c.lattice_units, 'ang')
lattice = [[6.0, 0.0, 0.0], [0.0, 6.0, 0.0], [0.0, 0.0, 6.0]]
self.assertTrue(
numpy.allclose(c.lattice, lattice, rtol=1e-05, atol=1e-08))
self.assertEqual(len(c.ions), 9)
self.assertEqual(len(c.ions.species('H')), 6)
self.assertEqual(len(c.ions.species('C')), 2)
self.assertEqual(len(c.ions.species('O')), 1)
C1 = c.ions.C1
self.assertEqual(len(c.ions.within(C1, 1.5)), 4)
def test_lattice_wrong_shape(self):
with self.assertRaises(cell.Cell.LatticeWrongShape):
c = cell.Cell(open(self.cell3_path).read())
import sys, os
import shutil
import random
import castepy.settings as settings
from castepy.input import cell
from castepy.calc import CastepCalc
from castepy.util import calc_from_path
psptest_path = os.path.join(settings.CASTEPY_ROOT, "templates/psptest")
merge_cell = cell.Cell(open(os.path.join(psptest_path, "psptest.cell")).read())
def make(source_ascpot, source_aeps, target_dir, **kwargs):
cell = merge_cell
s = os.path.split(source_ascpot)[1].split('_')[0]
cell.ions[0].s = s
target_name = s
dir_ncp = os.path.join(target_dir, 'ncp/')
dir_usp = os.path.join(target_dir, 'usp/')
if not os.path.isdir(dir_ncp):
os.mkdir(dir_ncp)
if not os.path.isdir(dir_usp):
os.mkdir(dir_usp)
cell_target = os.path.join(dir_usp, "%s.cell" % target_name)
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()
import sys, os, argparse
import shutil
import random
import castepy.settings as settings
from castepy.input import cell, parameters, pot
from castepy.calc import CastepCalc
from castepy.util import calc_from_path
nmr_path = os.path.join(settings.CASTEPY_ROOT, "templates/nmr")
merge_cell = cell.Cell(open(os.path.join(nmr_path, "nmr.cell")).read())
params = parameters.Parameters(
open(os.path.join(nmr_path, "nmr.param")).read())
import argparse
parser = argparse.ArgumentParser(
description='Create a CASTEP NMR calculation.')
parser.add_argument('source',
help='A cell file to build the calculation from.')
parser.add_argument('target_dir',
help='A directory to build the calculation in.')
parser.add_argument('-n',
'--num_cores',
type=int,
help='Number of cores to use.',
default=32)
parser.add_argument('-q',
'--queue',