def make_relaxed():
# Load data from results file
if (not os.path.isfile(g.files['relaxed'])):
g.end("No relaxed data - unable to continue.")
d = []
fh = open(g.files['relaxed'], 'r')
for line in fh:
d.append(line.strip())
fh.close()
nat = float(d[0])
a0 = float(d[1])
a0_scaled = float(d[2])
a0_scaled_bohr = float(d[3])
uv = numpy.zeros(
(
3,
3,
),
dtype=numpy.float64,
)
n = 4
for i in range(3):
for j in range(3):
uv[i, j] = float(d[n])
n = n + 1
vpa = float(d[13])
relaxed_energy_dft = float(d[14])
relaxed_energy = float(d[15])
relaxed_epa = float(d[16])
# Output
output.log("Making relaxed template using:", verbose=0)
output.log("{:20s} {:12.6f} ".format("Relaxed a0", a0), verbose=0)
output.log("{:20s} {:12.6f} ".format("Cx", g.ifile['cxyz'][0]),
verbose=0)
output.log("{:20s} {:12.6f} {:6s} ".format("Relaxed a0 (scaled)",
a0_scaled, 'angs'),
verbose=0)
output.log("{:20s} {:12.6f} {:6s}".format("Relaxed a0 (scaled)",
a0_scaled_bohr, 'bohr'),
verbose=0)
output.log("{:20s} {:12.6f} {:12.6f} {:12.6f} ".format(
"Relaxed UV", uv[0, 0], uv[0, 1], uv[0, 2]),
verbose=0)
output.log("{:20s} {:12.6f} {:12.6f} {:12.6f} ".format(
"", uv[1, 0], uv[1, 1], uv[1, 2]),
verbose=0)
output.log("{:20s} {:12.6f} {:12.6f} {:12.6f} ".format(
"", uv[2, 0], uv[2, 1], uv[2, 2]),
verbose=0)
t = template.load()
t.set_alat(a0_scaled_bohr)
t.set_cp_arr(uv)
t.save("template_relaxed.in", g.dirs['template'])
def run():
# Check file specified and that it exists
if (len(sys.argv) < 2):
g.end("ERROR. Please specifiy input file.")
if (not os.path.isfile(sys.argv[1])):
g.end("ERROR. Input file does not exist.")
# Load file
g.ifile['path'] = os.path.join(os.getcwd(), sys.argv[1])
ifile.load(g.ifile['path'])
def run():
output.log("", verbose=0)
output.log("", verbose=0)
output.log("Process Results", verbose=0)
output.log("##########################", verbose=0)
if (not os.path.isfile(g.files['relaxed'])):
g.end("No relaxed data - unable to continue.")
# Clear output
g.output = '#################################################################\n'
g.output = g.output + '# QEEOS Results #\n'
g.output = g.output + '#################################################################\n'
g.output = g.output + '\n'
process_results.relaxed()
process_results.eos_bm()
process_results.ec_mskp()
process_results.ec_rfkj()
fh = open(os.path.join(g.dirs['out'], "output.txt"), 'w')
fh.write(g.output)
fh.close()
def load(file_path):
output.log("Read input file", verbose=0)
# Default units
###############################################################
input_units = {
'energy': 'ev',
'length': 'ang',
'pressure': 'gpa',
}
# Read file
###############################################################
d = std.read(file_path)
# Loop over lines in file
###############################################################
for line in d:
f = line.split(" ")
f[0] = f[0].upper()
if (f[0] == "#TEMPLATE"):
template_file = os.path.abspath(f[1])
if (os.path.isfile(template_file)):
g.ifile['template'] = template_file
else:
g.end("ERROR. Template file does not exist.")
elif (f[0] == "#CONFIG"):
a0_units = None
a0 = None
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "STRUCTURE"):
g.ifile['structure'] = fn[1].lower()
elif (fn[0].upper() == "A0"):
a0 = float(fn[1])
elif (fn[0].upper() == "UNITS"):
a0_units = fn[1]
elif (fn[0].upper() == "CXYZ"):
g.ifile['cxyz'] = ds.config_cxyz(fn[1].split(","))
elif (fn[0].upper() == "LABELS"):
g.ifile['labels'] = fn[1].split(",")
if (a0 is not None):
if (a0_units is not None):
g.ifile['a0'] = units.convert(a0_units, 'angs', a0)
else:
g.ifile['a0'] = a0
elif (f[0] == "#DFTSETTINGS"):
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "ECUTWFC"):
g.ifile['ecutwfc'] = float(fn[1])
elif (fn[0].upper() == "ECUTRHO"):
g.ifile['ecutrho'] = float(fn[1])
elif (fn[0].upper() == "KPOINTS"):
g.ifile['kpoints'] = ds.kpoints(fn[1])
elif (fn[0].upper() == "DEGAUSS"):
g.ifile['degauss'] = float(fn[1])
elif (f[0] == "#RELAX"):
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "RUN"):
g.ifile['relax'] = True
if (fn[1][0].upper() == "F"):
g.ifile['relax'] = False
elif (f[0] == "#EOS_BM"):
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "RUN"):
g.ifile['eos_bm'] = True
if (fn[1][0].upper() == "F"):
g.ifile['eos_bm'] = False
elif (fn[0].upper() == "STRAIN"):
g.ifile['eos_bm_strain'] = float(fn[1])
elif (fn[0].upper() == "STEPS"):
g.ifile['eos_bm_steps'] = int(fn[1])
elif (fn[0].upper() == "CALC"):
g.ifile['eos_bm_calc'] = fn[1].lower()
elif (f[0] == "#EC_MSKP"):
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "RUN"):
g.ifile['ec_mskp'] = True
if (fn[1][0].upper() == "F"):
g.ifile['ec_mskp'] = False
elif (fn[0].upper() == "STRAIN"):
g.ifile['ec_mskp_strain'] = float(fn[1])
elif (fn[0].upper() == "STEPS"):
g.ifile['ec_mskp_steps'] = int(fn[1])
elif (fn[0].upper() == "CALC"):
g.ifile['ec_mskp_calc'] = fn[1].lower()
elif (f[0] == "#EC_RFKJ"):
for fn in f:
fn = fn.split("=")
if (fn[0].upper() == "RUN"):
g.ifile['ec_rfkj'] = True
if (fn[1][0].upper() == "F"):
g.ifile['ec_rfkj'] = False
elif (fn[0].upper() == "STRAIN"):
g.ifile['ec_rfkj_strain'] = float(fn[1])
elif (fn[0].upper() == "STEPS"):
g.ifile['ec_rfkj_steps'] = int(fn[1])
elif (fn[0].upper() == "CALC"):
g.ifile['ec_rfkj_calc'] = fn[1].lower()
elif (f[0] == "#DFTADJUST"):
for fn in f:
if ("=" in fn):
print(fn)
fn = fn.split("=")
label = fn[0].strip().upper()
fd = fn[1].split(',')
if (len(fd) == 4):
dft_energy = units.convert(fd[1], 'ev',
float(fd[0]))
known_energy = units.convert(
fd[3], 'ev', float(fd[2]))
g.adjust[label] = known_energy - dft_energy
def end():
g.end(msg=None)