def test_fmax(self):
" Make sure we can get correct max forces. "
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
coords, forces = outcar.forces()
ret_index, ret_max_force = outcar.fmax(forces)
ref_index = 4
ref_max_force = [-0.0, -0.0, -0.046234]
self.assertEqual(ret_index, ref_index)
self.assertListEqual(ret_max_force, ref_max_force)
def test_fmax(self):
" Make sure we can get correct max forces. "
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
coords, forces = outcar.forces()
ret_index, ret_max_force = outcar.fmax(forces)
ref_index = 4
ref_max_force = [-0.0, -0.0, -0.046234]
self.assertEqual(ret_index, ref_index)
self.assertListEqual(ret_max_force, ref_max_force)
def test_forces(self):
" Make sure we can get correct forces data."
# {{{
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
coords, forces = outcar.forces()
ref_coords = [[1.78441, 0.85618, 2.29204], [0.16369, 0.85618, 4.56647],
[0.97405, -0.5474, 0.0], [0.97405, -0.5474, 6.88358],
[4.21548, -0.5474, 2.29204], [2.59476, -0.5474, 4.56647],
[3.40512, -1.95098, 0.0], [3.40512, -1.95098, 6.88358],
[6.64655, -1.95098,
2.29204], [5.02584, -1.95098, 4.56647],
[5.83619, -3.35456, 0.0], [5.83619, -3.35456, 6.88358],
[1.78441, 3.66334, 2.29204], [0.16369, 3.66334, 4.56647],
[0.97405, 2.25976, 0.0], [0.97405, 2.25976, 6.88358],
[4.21548, 2.25976, 2.29204], [2.59476, 2.25976, 4.56647],
[3.40512, 0.85618, 0.0], [3.40512, 0.85618, 6.88358],
[6.64655, 0.85618, 2.29204], [5.02584, 0.85618, 4.56647],
[5.83619, -0.5474, 0.0], [5.83619, -0.5474, 6.88358],
[1.78441, 6.4705, 2.29204], [0.16369, 6.4705, 4.56647],
[0.97405, 5.06692, 0.0], [0.97405, 5.06692, 6.88358],
[4.21548, 5.06692, 2.29204], [2.59476, 5.06692, 4.56647],
[3.40512, 3.66334, 0.0], [3.40512, 3.66334, 6.88358],
[6.64655, 3.66334, 2.29204], [5.02584, 3.66334, 4.56647],
[5.83619, 2.25976, 0.0], [5.83619, 2.25976, 6.88358]]
ref_forces = [[0.0, -0.0, 0.136895], [0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895], [-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895], [-0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895], [0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895], [-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895], [-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895], [0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895], [-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895], [0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126], [-0.0, 0.0, -0.046234]]
ret_coords, ret_forces = outcar.forces()
self.assertListEqual(ref_coords, ret_coords)
self.assertListEqual(ref_forces, ret_forces)
def test_mask_forces(self):
" Test private helper function __mask_forces()."
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
tfs = [["T", "T", "T"], ["F", "F", "F"], ["F", "T", "F"]]
forces = [[1.78441, 0.85618, 2.29204], [0.16369, 0.85618, 4.56647],
[0.97405, -0.5474, 0.0]]
ref_masked_forces = [[1.78441, 0.85618, 2.29204], [0.0, 0.0, 0.0],
[0.0, -0.5474, 0.0]]
ret_masked_forces = outcar._OutCar__mask_forces(forces, tfs)
self.assertListEqual(ref_masked_forces, ret_masked_forces)
def test_zpe(self):
" Make sure we can get correct ZPE. "
filename = path + "/OUTCAR_freq"
poscar = path + "/POSCAR_freq"
outcar = OutCar(filename=filename, poscar=poscar)
ref_zpe = 0.1117761635
ret_zpe = outcar.zpe
self.assertEqual(ref_zpe, ret_zpe)
# Check OUTCAR without freq info.
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
self.assertFalse(hasattr(outcar, "zpe"))
def test_mask_forces(self):
" Test private helper function __mask_forces()."
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
tfs = [["T", "T", "T"],
["F", "F", "F"],
["F", "T", "F"]]
forces = [[1.78441, 0.85618, 2.29204],
[0.16369, 0.85618, 4.56647],
[0.97405, -0.5474, 0.0]]
ref_masked_forces = [[1.78441, 0.85618, 2.29204],
[0.0, 0.0, 0.0],
[0.0, -0.5474, 0.0]]
ret_masked_forces = outcar._OutCar__mask_forces(forces, tfs)
self.assertListEqual(ref_masked_forces, ret_masked_forces)
def test_freq_types(self):
" Make sure we can get correct frequency types. "
filename = path + "/OUTCAR_freq"
poscar = path + "/POSCAR_freq"
outcar = OutCar(filename=filename, poscar=poscar)
ref_freq_types = [["f", "f", "f"], ["f", "f", "f/i"]]
ret_freq_types = outcar.freq_types
self.assertListEqual(ref_freq_types, ret_freq_types)
def test_construction_query(self):
" Test OutCar construction and query functions. "
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename, poscar=poscar)
# Check query functions.
self.assertEqual(outcar.filename, filename)
self.assertTrue(isinstance(outcar.poscar, PosCar))
# Check lazy property.
ref_total_forces = [
0.24345800000000001, 0.16800399999999999, 0.103559,
0.046233999999999997
]
ret_total_forces = outcar.total_forces
self.assertListEqual(ref_total_forces, ret_total_forces)
self.assertEqual(outcar.last_max_force, 0.046233999999999997)
self.assertEqual(outcar.last_max_atom, 4)
def test_freq_iterator(self):
" Make sure we can get correct frequency iterator. "
filename = path + "/OUTCAR_freq"
poscar = path + "/POSCAR_freq"
outcar = OutCar(filename=filename, poscar=poscar)
freq_iter = outcar.freq_iterator
ret_freq_dict = next(freq_iter)
# Check.
ref_meV = "93.954209"
ret_meV = ret_freq_dict["meV"]
self.assertEqual(ref_meV, ret_meV)
ref_cm = "757.791533"
ret_cm = ret_freq_dict["cm-1"]
self.assertEqual(ref_cm, ret_cm)
ref_THz = "22.718019"
ret_THz = ret_freq_dict["THz"]
self.assertEqual(ref_THz, ret_THz)
ref_PiTHz = "142.741525"
ret_PiTHz = ret_freq_dict["2PiTHz"]
self.assertEqual(ref_PiTHz, ret_PiTHz)
ref_index = "1"
ret_index = ret_freq_dict["index"]
self.assertEqual(ref_index, ret_index)
ref_freq_type = "f"
ret_freq_type = ret_freq_dict["freq_type"]
self.assertEqual(ref_freq_type, ret_freq_type)
ref_coord = (2.795628, 0.856184, 1.196977)
ret_coord = ret_freq_dict["coordinates"][0]
self.assertTupleEqual(ref_coord, ret_coord)
ref_delta = (0.078066, -0.028474, 0.674474)
ret_delta = ret_freq_dict["deltas"][-1]
self.assertTupleEqual(ref_delta, ret_delta)
def test_forces(self):
" Make sure we can get correct forces data."
# {{{
filename = path + "/OUTCAR"
poscar = path + "/POSCAR"
outcar = OutCar(filename=filename,
poscar=poscar)
coords, forces = outcar.forces()
ref_coords = [[1.78441, 0.85618, 2.29204],
[0.16369, 0.85618, 4.56647],
[0.97405, -0.5474, 0.0],
[0.97405, -0.5474, 6.88358],
[4.21548, -0.5474, 2.29204],
[2.59476, -0.5474, 4.56647],
[3.40512, -1.95098, 0.0],
[3.40512, -1.95098, 6.88358],
[6.64655, -1.95098, 2.29204],
[5.02584, -1.95098, 4.56647],
[5.83619, -3.35456, 0.0],
[5.83619, -3.35456, 6.88358],
[1.78441, 3.66334, 2.29204],
[0.16369, 3.66334, 4.56647],
[0.97405, 2.25976, 0.0],
[0.97405, 2.25976, 6.88358],
[4.21548, 2.25976, 2.29204],
[2.59476, 2.25976, 4.56647],
[3.40512, 0.85618, 0.0],
[3.40512, 0.85618, 6.88358],
[6.64655, 0.85618, 2.29204],
[5.02584, 0.85618, 4.56647],
[5.83619, -0.5474, 0.0],
[5.83619, -0.5474, 6.88358],
[1.78441, 6.4705, 2.29204],
[0.16369, 6.4705, 4.56647],
[0.97405, 5.06692, 0.0],
[0.97405, 5.06692, 6.88358],
[4.21548, 5.06692, 2.29204],
[2.59476, 5.06692, 4.56647],
[3.40512, 3.66334, 0.0],
[3.40512, 3.66334, 6.88358],
[6.64655, 3.66334, 2.29204],
[5.02584, 3.66334, 4.56647],
[5.83619, 2.25976, 0.0],
[5.83619, 2.25976, 6.88358]]
ref_forces = [[0.0, -0.0, 0.136895],
[0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895],
[-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895],
[-0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895],
[0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895],
[-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895],
[-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, -0.0, -0.046234],
[0.0, -0.0, 0.136895],
[0.0, -0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895],
[-0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, 0.0, -0.046234],
[0.0, -0.0, 0.136895],
[0.0, 0.0, 0.008464],
[0.0, -0.0, -0.099126],
[-0.0, 0.0, -0.046234]]
ret_coords, ret_forces = outcar.forces()
self.assertListEqual(ref_coords, ret_coords)
self.assertListEqual(ref_forces, ret_forces)
import numpy as np
from vaspy.iter import OutCar
from vaspy.matstudio import XsdFile
from vaspy.functions import str2list
_logger = logging.getLogger("vaspy.script")
# Set arguments parser.
parser = argparse.ArgumentParser()
parser.add_argument("--xsd", help="create MaterStudio .xsd file",
action="store_true")
args = parser.parse_args()
outcar = OutCar()
pos, forces = outcar.forces(-1)
idx = outcar.last_max_atom - 1
pos = pos[idx]
forces = forces[idx]
_logger.info("{:<15s}: {}".format("max force atom", outcar.last_max_atom))
_logger.info("{:<15s}: ({}, {}, {})".format("atom position", *pos))
_logger.info("{:<15s}: {}, {}, {}".format("forces", *forces))
_logger.info("{:<15s}: {}\n".format("total-force", outcar.last_max_force))
# Get fort.188 info.
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
_logger.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE"))
import sys
import numpy as np
from vaspy.iter import OutCar
from vaspy.matstudio import XsdFile
from vaspy.functions import str2list
# Set arguments parser.
parser = argparse.ArgumentParser()
parser.add_argument("--xsd",
help="create MaterStudio .xsd file",
action="store_true")
args = parser.parse_args()
outcar = OutCar()
max_num = outcar.max_force_atom
force_info = outcar.atom_forces[max_num - 1, :]
pos = force_info[:3].tolist()
forces = force_info[3:].tolist()
logging.info("{:<15s}: {}".format("max force atom", max_num))
logging.info("{:<15s}: ({}, {}, {})".format("atom position", *pos))
logging.info("{:<15s}: {}, {}, {}".format("forces", *forces))
logging.info("{:<15s}: {}\n".format("total-force", np.linalg.norm(forces)))
# Get fort.188 info.
if os.path.exists('./fort.188'):
with open('fort.188', 'r') as f:
atom_info = f.readlines()[5]
logging.info("{:<10s}{:<10s}{:<15s}".format("Atom1", "Atom2", "DISTANCE"))
from vaspy.incar import InCar
from vaspy.atomco import PosCar
from vaspy.iter import OutCar
from vaspy.matstudio import XsdFile
from vaspy.functions import str2list
_logger = logging.getLogger("vaspy.script")
# Set arguments parser.
parser = argparse.ArgumentParser()
parser.add_argument("--xsd",
help="create MaterStudio .xsd file",
action="store_true")
args = parser.parse_args()
outcar = OutCar()
poses, forces = outcar.forces(-1)
poscar = PosCar()
tfs = poscar.tf
incar = InCar()
#print(incar.paras)
EDIFFG = incar.get_pvalue('EDIFFG')
#EDIFFG = 0.05
bad_ids = []
max_idx = [-1, -1, -1]
max_force = [0., 0., 0.]
for i, (pos, force, tf) in enumerate(zip(poses, forces, tfs)):
for j, (c, f) in enumerate(zip(tf, force)):