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add full periodic table and remove deprecation warnings
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add full periodic table and remove deprecation warnings
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@skuschel
skuschel authored Nov 24, 2023
2 parents de60a34 + 2c3baae commit 7a7af8a
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Showing 5 changed files with 52 additions and 30 deletions.
2 changes: 1 addition & 1 deletion postpic/_compat/functions.py
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Expand Up @@ -24,7 +24,7 @@

import numpy as np
import scipy as sp
import scipy.signal as sps
import scipy.signal.windows as sps
import collections

try:
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4 changes: 2 additions & 2 deletions postpic/datahandling.py
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Expand Up @@ -2016,10 +2016,10 @@ def fft(self, axes=None, exponential_signs='spatial', old_behaviour=False, **kwa
dx = {i: self.axes[i].spacing for i in axes}

# Unit volume of transform
dV = np.product(list(dx.values()))
dV = np.prod(list(dx.values()))

# Number of grid cells of transform
N = np.product([self.shape[i] for i in axes])
N = np.prod([self.shape[i] for i in axes])

# Total volume of transform
V = dV*N
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36 changes: 29 additions & 7 deletions postpic/particles/_routines.py
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Expand Up @@ -189,13 +189,35 @@ def _specdict(mass, charge, ision):
'gold20': _specdict(1836.2 * 197, 20, True)}

# unit: amu
_masslistelement = {'H': 1, 'He': 4,
'Li': 6.9, 'C': 12, 'N': 14, 'O': 16, 'F': 19, 'Ne': 20.2,
'Na': 23, 'Al': 27, 'Si': 28, 'S': 32, 'Cl': 35.5, 'Ar': 40,
'Ti': 47.9, 'Cr': 52, 'Fe': 55.8, 'Cu': 63.5, 'Zn': 65.4, 'Kr': 83.8,
'Rb': 85.5, 'Zr': 91.2, 'Pd': 106.4, 'Ag': 107.8, 'Sn': 118.7,
'Xe': 131.3,
'W': 183.8, 'Pt': 195, 'Au': 197, 'Hg': 200.6, 'Pb': 207.2}
_masslistelement = {'H': 1.008, 'He': 4.003, 'Li': 6.941, 'Be': 9.012,
'B': 10.811, 'C': 12.011, 'N': 14.007, 'O': 15.999,
'F': 18.998, 'Ne': 20.180, 'Na': 22.990, 'Mg': 24.305,
'Al': 26.982, 'Si': 28.086, 'P': 30.974, 'S': 32.066,
'Cl': 35.453, 'Ar': 39.948, 'K': 39.098, 'Ca': 40.078,
'Sc': 44.956, 'Ti': 47.867, 'V': 50.942, 'Cr': 51.996,
'Mn': 54.938, 'Ff': 55.845, 'Co': 58.933, 'Ni': 58.693,
'Cu': 63.546, 'Zn': 65.38, 'Ga': 69.723, 'Ge': 72.631,
'As': 74.922, 'Se': 78.971, 'Br': 79.904, 'Kr': 84.798,
'Rb': 84.468, 'Sr': 87.62, 'Y': 88.906, 'Zr': 91.224,
'Nb': 92.906, 'Mo': 95.95, 'Tc': 98.907, 'Ru': 101.07,
'Rh': 102.906, 'Pd': 106.42, 'Ag': 107.868, 'Cd': 112.414,
'In': 114.818, 'Sm': 118.711, 'Sb': 121.760, 'Te': 126.7,
'I': 126.904, 'Xe': 131.294, 'Cs': 132.905, 'Ba': 137.328,
'La': 138.905, 'Ce': 140.116, 'Pr': 140.908, 'Nd': 144.243,
'Pm': 144.913, 'Sm': 150.36, 'Eu': 151.964, 'Gd': 157.25,
'Tb': 158.925, 'Dy': 162.500, 'Ho': 164.930, 'Er': 167.259,
'Tm': 168.934, 'Yb': 173.055, 'Lu': 174.967, 'Hf': 178.49,
'Ta': 180.948, 'W': 183.84, 'Rr': 186.207, 'Os': 190.23,
'Ir': 192.217, 'Pt': 195.085, 'Au': 196.967, 'Hg': 200.592,
'Tl': 204.383, 'Pb': 207.2, 'Bi': 208.980, 'Po': 208.982,
'At': 209.987, 'Rn': 222.081, 'Fr': 223.020, 'Ra': 226.025,
'Ac': 227.028, 'Th': 232.038, 'Pa': 231.036, 'U': 238.029,
'Np': 237, 'Pu': 244, 'Am': 243, 'Cm': 247, 'Bk': 247,
'Ct': 251, 'Es': 252, 'Fm': 257, 'Md': 258, 'No': 259,
'Lr': 262, 'Rf': 261, 'Db': 262, 'Sg': 266, 'Bh': 264,
'Hs': 269, 'Mt': 268, 'Ds': 271, 'Rg': 272, 'Cn': 285,
'Nh': 284, 'Fl': 289, 'Mc': 288, 'Lv': 292, 'Ts': 294,
'Og': 294}

@staticmethod
def isejected(species):
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10 changes: 5 additions & 5 deletions postpic/particles/particles.py
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Expand Up @@ -145,7 +145,7 @@ def _readatomic(self, key):
ret = self._dumpreader.getSpecies(self.species, key)
# now that we have got the data, check if compress was used and/or maybe cache value
ret = np.int64(ret) if key == 'id' else np.float64(ret)
if ret.shape is (): # cache single scalars always
if ret.shape == (): # cache single scalars always
self._cache[key] = ret
elif self._compressboollist is not None:
ret = ret[self._compressboollist] # avoid executing this line too often.
Expand Down Expand Up @@ -227,7 +227,7 @@ def _compress_bool(self, condition):
else:
ret._compressboollist[ret._compressboollist] = condition
for key in ret._cache:
if ret._cache[key].shape is not ():
if ret._cache[key].shape != ():
ret._cache[key] = ret._cache[key][condition]
return ret

Expand Down Expand Up @@ -257,7 +257,7 @@ def __invert__(self):
ret._cache = {} # clear cache
if self._compressboollist is None:
ret._compressboollist = np.asarray(False)
elif self._compressboollist.shape is () and bool(self._compressboollist) is False:
elif self._compressboollist.shape == () and bool(self._compressboollist) is False:
ret._compressboollist = None
else:
ret._compressboollist = ~self._compressboollist
Expand All @@ -267,7 +267,7 @@ def __invert__(self):
# --- Only very basic functions

def __len__(self): # = number of particles
# find a valid dataset to count number of paricles
# find a valid dataset to count number of particles
# return 0 if no valid dataset can be found
ret = 0
if self._compressboollist is not None:
Expand Down Expand Up @@ -662,7 +662,7 @@ def __call_sp(self, sp):
# sp MUST be ScalarProperty
def ssdata(ss):
a = ss(sp)
if a.shape is ():
if a.shape == ():
a = np.repeat(a, len(ss))
return a
if len(self._ssas) == 0:
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30 changes: 15 additions & 15 deletions test/test_helper.py
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Expand Up @@ -25,14 +25,14 @@ def checkion(self, data, m, c, eject, tracer, ision):
def test_identifyspecies_ion(self):
idfy = pp.identifyspecies
self.checkion(idfy('proton'), 1, 1, False, False, True)
self.checkion(idfy('H1'), 1, 1, False, False, True)
self.checkion(idfy('tracer_O3'), 16, 3, False, True, True)
self.checkion(idfy('ejected_tracer_C4'), 12, 4, True, True, True)
self.checkion(idfy('H1'), 1.008, 1, False, False, True)
self.checkion(idfy('tracer_O3'), 15.999, 3, False, True, True)
self.checkion(idfy('ejected_tracer_C4'), 12.011, 4, True, True, True)
self.checkion(idfy('ionm3c7'), 3, 7, False, False, True)
self.checkion(idfy('ionm30c70xx5'), 30, 70, False, False, True)
self.checkion(idfy('tracer_ejected_Au27a'), 197, 27, True, True, True)
self.checkion(idfy('ejected_tracer_Au27'), 197, 27, True, True, True)
self.checkion(idfy('tracer_blahh_Au27x'), 197, 27, False, True, True)
self.checkion(idfy('tracer_ejected_Au27a'), 196.967, 27, True, True, True)
self.checkion(idfy('ejected_tracer_Au27'), 196.967, 27, True, True, True)
self.checkion(idfy('tracer_blahh_Au27x'), 196.967, 27, False, True, True)

def test_identifyspecies_electron(self):
idfy = pp.identifyspecies
Expand All @@ -58,17 +58,17 @@ def test_identifyspecies_praefix(self):
self.assertEqual(x['w'], True)
self.assertEqual(x['33'], True)
self.assertEqual(x['He5'], True)
self.checkion(x, 16,3, False, True, True)
self.checkion(x, 15.999,3, False, True, True)

def test_identifyspecies_extendedsyntax(self):
idfy = pp.identifyspecies
self.checkion(idfy('H'), 1, 0, False, False, True)
self.checkion(idfy('HPlus'), 1, 1, False, False, True)
self.checkion(idfy('H1Plus'), 1, 1, False, False, True)
self.checkion(idfy('H'), 1.008, 0, False, False, True)
self.checkion(idfy('HPlus'), 1.008, 1, False, False, True)
self.checkion(idfy('H1Plus'), 1.008, 1, False, False, True)
#self.checkion(idfy('Hplus'), 1, 1, False, False, True)
self.checkion(idfy('HePlusPlus'), 4, 2, False, False, True)
self.checkion(idfy('He2Plus'), 4, 2, False, False, True)
self.checkion(idfy('HPlus'), 1, 1, False, False, True)
self.checkion(idfy('HePlusPlus'), 4.003, 2, False, False, True)
self.checkion(idfy('He2Plus'), 4.003, 2, False, False, True)
self.checkion(idfy('HPlus'), 1.008, 1, False, False, True)
self.checke(idfy('HElectron'), 1, -1, False, False, False)
self.checke(idfy('HElectrons'), 1, -1, False, False, False)
self.checke(idfy('HElec'), 1, -1, False, False, False)
Expand All @@ -81,10 +81,10 @@ def test_falsefriends(self):
self.checke(idfy('HElectron'), 1, -1, False, False, False)
self.checke(idfy('HeElectron'), 1, -1, False, False, False)
self.checke(idfy('Heelectron'), 1, -1, False, False, False)
self.checkion(idfy('Helectron'), 4, 0, False, False, True)
self.checkion(idfy('Helectron'), 4.003, 0, False, False, True)
# Tiny differences may decide about Ne or electrons
self.checke(idfy('NElectron'), 1, -1, False, False, False)
self.checkion(idfy('Nelectron'), 20.2, 0, False, False, True)
self.checkion(idfy('Nelectron'), 20.180, 0, False, False, True)
self.checke(idfy('Neelectron'), 1, -1, False, False, False)


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