def test_out():
assert (round(out.elastic_props()["KV"], 2)) == (87.27)
out_efg = Outcar(
os.path.join(os.path.dirname(__file__), "OUTCAR.EFG-JVASP-12148"))
assert out_efg.efg_tensor_diag[0][0] == -4.766
assert out_efg.quad_mom[0][0] == 0.023
assert out_efg.converged == True
td = out_efg.to_dict()
fd = Outcar.from_dict(td)
def test_dfpt():
vrun = Vasprun(
os.path.join(os.path.dirname(__file__), "vasprun.xml.JVASP-39"))
out = Outcar(os.path.join(os.path.dirname(__file__), "OUTCAR.JVASP-39"))
bec = round(vrun.dfpt_data["born_charges"][0][0][0], 2)
eig = round(out.phonon_eigenvalues[2], 2)
ionic_pz, total_pz = out.piezoelectric_tensor
pz = total_pz[2][0]
assert (bec, eig, pz) == (2.52, 19.58, -0.26756)
# print (vrun.all_stresses)
assert vrun.all_stresses[0][0][0] == -14.79381147
assert vrun.all_forces[0][0][0] == 0
assert vrun.all_energies[0] == -24.86360178
assert vrun.all_structures[0].volume == 42.60334334259966
def test_ir():
vrun = Vasprun(
os.path.join(os.path.dirname(__file__), "vasprun.xml.JVASP-39"))
out = Outcar(os.path.join(os.path.dirname(__file__), "OUTCAR.JVASP-39"))
phonon_eigenvectors = vrun.dfpt_data["phonon_eigenvectors"]
vrun_eigs = vrun.dfpt_data["phonon_eigenvalues"]
phonon_eigenvalues = out.phonon_eigenvalues
masses = vrun.dfpt_data["masses"]
born_charges = vrun.dfpt_data["born_charges"]
x, y = ir_intensity(
phonon_eigenvectors=phonon_eigenvectors,
phonon_eigenvalues=phonon_eigenvalues,
masses=masses,
born_charges=born_charges,
)
assert round(y[2], 2) == 0
def test_out():
assert (round(out.elastic_props()["KV"], 2)) == (87.27)
out_efg = Outcar(
os.path.join(os.path.dirname(__file__), "OUTCAR.EFG-JVASP-12148"))
out_efg_raw = Outcar(
os.path.join(os.path.dirname(__file__),
"OUTCAR.EFG-JVASP-12148")).efg_raw_tensor
assert out_efg.efg_tensor_diag()[0][0] == -4.766
assert out_efg.efg_tensor_diag(std_conv=False)[0][0] == -4.766
assert out_efg.quad_mom[0][0] == 0.023
assert out_efg.converged == True
td = out_efg.to_dict()
fd = Outcar.from_dict(td)
print("out_efg_raw", (out_efg_raw))
print()
print("out_efg_raw", np.linalg.eig(out_efg_raw)[0])
print()
print("out_efg", out_efg.efg_tensor_diag())
print()
from jarvis.io.vasp.outputs import Vasprun, Outcar
from jarvis.analysis.phonon.ir import ir_intensity, ir_intensity_phonopy
import os
import shutil
out = Outcar(
os.path.join(os.path.dirname(__file__), "..", "..", "io", "vasp",
"OUTCAR.JVASP-39"))
vrun_file = os.path.join(
os.path.dirname(__file__),
"..",
"..",
"io",
"vasp",
"vasprun.xml.JVASP-39",
)
dirc = os.path.join(
os.path.dirname(__file__),
"..",
"..",
"io",
"vasp",
)
vrun = Vasprun(vrun_file)
def test_ir():
phonon_eigenvectors = vrun.dfpt_data["phonon_eigenvectors"]
vrun_eigs = vrun.dfpt_data["phonon_eigenvalues"]
phonon_eigenvalues = out.phonon_eigenvalues
"examples",
"vasp",
"SiOptb88",
"SiOptb88",
"MAIN-RELAX-bulk@mp_149",
"OSZICAR",
)
)
out = Outcar(
filename=os.path.join(
os.path.dirname(__file__),
"..",
"..",
"..",
"..",
"examples",
"vasp",
"SiOptb88",
"SiOptb88",
"MAIN-ELASTIC-bulk@mp_149",
"OUTCAR",
)
)
wder = Waveder(
os.path.join(
os.path.dirname(__file__),
"..",
"..",
"..",
"..",
"examples",
def runjob(self):
"""Provide main function for running a generic VASP calculation."""
# poscar=self.poscar
# incar=self.incar
# kpoints=self.kpoints
# copy_files=self.copy_files
# cwd = str(os.getcwd())
if self.jobname == "":
jobname = str(self.poscar.comment)
# job_dir = str(self.jobname)
run_file = (str(os.getcwd()) + str("/") + str(self.jobname) +
str(".json"))
run_dir = str(os.getcwd()) + str("/") + str(self.jobname)
if self.poscar.comment.startswith("Surf"):
[a, b, c] = self.kpoints.kpts[0]
# self.kpoints.kpts = [[a, b, 1]]
self.kpoints = Kpoints3D(kpoints=[[a, b, 1]])
try:
pol = self.poscar.atoms.check_polar
if pol:
COM = self.poscar.atoms.get_center_of_mass()
print("COM=", COM)
print("Found polar surface,setting dipole corrections")
self.incar.update({
"LDIPOL":
".TRUE.",
"IDIPOL":
3,
"ISYM":
0,
"DIPOL":
str(COM[0]) + str(" ") + str(COM[2]) + str(" ") +
str(COM[2]),
})
print(
"Polar surface encountered in run_job",
self.poscar.comment,
)
except Exception:
pass
wait = False
json_file = str(self.jobname) + str(".json")
print(
"json should be here=",
str(os.getcwd()) + str("/") + str(json_file),
)
print("json should be=", json_file, run_file, os.getcwd())
if os.path.exists(str(os.getcwd()) + str("/") + str(json_file)):
try:
data_cal = loadjson(
str(os.getcwd()) + str("/") + str(json_file))
tmp_outcar = (str(os.getcwd()) + str("/") +
str(json_file.split(".json")[0]) +
str("/OUTCAR"))
print("outcar is", tmp_outcar)
wait = Outcar(tmp_outcar).converged # True
print("outcar status", wait)
if wait:
f_energy = data_cal[0]["final_energy"]
contcar = (str(os.getcwd()) + str("/") +
str(json_file.split(".json")[0]) +
str("/CONTCAR"))
return f_energy, contcar
except Exception:
pass
attempt = 0
while not wait:
attempt = attempt + 1
if attempt == self.attempts:
wait = True
# print("Setting up POTCAR")
# if self.potcar is None:
# new_symb = list(set(self.poscar.atoms.elements))
# self.potcar = Potcar(elements=new_symb, pot_type=self.pot_type)
if not os.path.exists(run_dir):
print("Starting new job")
os.makedirs(run_dir)
os.chdir(run_dir)
self.poscar.write_file("POSCAR")
else:
os.chdir(run_dir)
if os.path.isfile("OUTCAR"):
try:
wait = Outcar(
"OUTCAR"
).converged # Vasprun("vasprun.xml").converged
# wait=Vasprun("vasprun.xml").converged
except Exception:
pass
try:
self.potcar.write_file("POTCAR")
print("FOUND OLD CONTCAR in", os.getcwd())
copy_cmd = str("cp CONTCAR POSCAR")
self.poscar.write_file("POSCAR")
# pos = Poscar.from_file("CONTCAR")
print("copy_cmd=", copy_cmd)
if ("ELAST" not in jobname
and "LEPSILON" not in jobname):
# Because in ELASTIC calculations
# structures are deformed
os.system(copy_cmd)
# time.sleep(3)
except Exception:
pass
self.incar.write_file("INCAR")
self.potcar.write_file("POTCAR")
self.kpoints.write_file("KPOINTS")
for i in self.copy_files:
print("copying", i)
shutil.copy2(i, "./")
self.run() # .wait()
print("Queue 1")
if os.path.isfile("OUTCAR"):
try:
wait = Outcar(
"OUTCAR").converged # Vasprun("vasprun.xml").converged
except Exception:
pass
print("End of the first loop", os.getcwd(), wait)
f_energy = "na"
# enp = "na"
contcar = str(os.getcwd()) + str("/") + str("CONTCAR")
final_str = Poscar.from_file(contcar).atoms
vrun = Vasprun("vasprun.xml")
f_energy = float(vrun.final_energy)
# enp = float(f_energy) / float(final_str.num_atoms)
# natoms = final_str.num_atoms
os.chdir("../")
if wait:
data_cal = []
data_cal.append({
"jobname": self.jobname,
"poscar": self.poscar.atoms.to_dict(),
"incar": self.incar.to_dict(),
"kpoints": self.kpoints.to_dict(),
"final_energy": (f_energy),
"contcar": final_str.to_dict(),
})
json_file = str(self.jobname) + str(".json")
f_json = open(json_file, "w")
f_json.write(json.dumps(data_cal))
f_json.close()
print("Wrote json file", f_energy)
return f_energy, contcar
def test_vasp_et():
out = Outcar(outcar)
et = ElasticTensor(out.elastic_props()["cij"])
print(et.to_dict())