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General lint and formatting #6

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Mar 27, 2024
Merged

General lint and formatting #6

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2 changes: 1 addition & 1 deletion notebooks/Zn-EDTA
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Original file line number Diff line number Diff line change
Expand Up @@ -213,4 +213,4 @@ Tit 3
10.0480 -296.5 0
10.2402 -297.9 0
10.4345 -299.2 0
10.6300 -300.6 1
10.6300 -300.6 1
19 changes: 11 additions & 8 deletions notebooks/multidimensinal_matrix.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,7 @@
"source": [
"import numpy as np\n",
"from libeq.data_structure import SolverData\n",
"from libeq import EqSolver\n",
"from libeq.solver import species_concentration, fobj, damping\n",
"import numpy as np\n",
"from libeq.solver import species_concentration\n",
"\n",
"# Create SolverData object\n",
"solver_data = SolverData.load_from_bstac(\n",
Expand Down Expand Up @@ -152,7 +150,7 @@
"c1 = c\n",
"c2 = species_concentration(c, log_beta, stoichiometry, solid_stoichiometry)\n",
"\n",
"c1 + np.sum(c2[:,np.newaxis,:]*stoichiometry[np.newaxis, ...],axis=2) - c"
"c1 + np.sum(c2[:, np.newaxis, :] * stoichiometry[np.newaxis, ...], axis=2) - c"
]
},
{
Expand All @@ -174,7 +172,12 @@
}
],
"source": [
"(species_concentration(c, log_beta, stoichiometry, solid_stoichiometry, full=True)[:,np.newaxis,:] * full_stoichiometry).sum(axis=2)"
"(\n",
" species_concentration(c, log_beta, stoichiometry, solid_stoichiometry, full=True)[\n",
" :, np.newaxis, :\n",
" ]\n",
" * full_stoichiometry\n",
").sum(axis=2)"
]
},
{
Expand All @@ -187,7 +190,7 @@
"arr = np.arange(32).reshape(2, 16)\n",
"\n",
"# Create a diagonal matrix from the rows of the array using broadcasting\n",
"diag_matrices = np.einsum('ij,jk->ijk', arr, np.eye(arr.shape[1]))"
"diag_matrices = np.einsum(\"ij,jk->ijk\", arr, np.eye(arr.shape[1]))"
]
},
{
Expand Down Expand Up @@ -225,8 +228,8 @@
"J = stoichiometry @ diag_matrices @ stoichiometry.T\n",
"\n",
"diagonal_indices = np.diag_indices(J.shape[1])\n",
"J[:,diagonal_indices[0], diagonal_indices[1]] += arr[:, :3]\n",
"J\n"
"J[:, diagonal_indices[0], diagonal_indices[1]] += arr[:, :3]\n",
"J"
]
},
{
Expand Down
19 changes: 9 additions & 10 deletions notebooks/staco4.inp
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Original file line number Diff line number Diff line change
Expand Up @@ -46,17 +46,17 @@ _________________Input File______________________
=1: if the ionic strength varies in some titrations or if different
titrations were performed at different ionic strengths
=2: as ICD=1, but C,D and E for E0 are given as input
WESP: weights=1/DV^wesp
If WESP>0, calculations are performed two steps. The first is
the normal one - according to the given input instructions -.
The second step, the calculations are performed giving each point
a new weight on the basis of the residual calculated in the first
WESP: weights=1/DV^wesp
If WESP>0, calculations are performed two steps. The first is
the normal one - according to the given input instructions -.
The second step, the calculations are performed giving each point
a new weight on the basis of the residual calculated in the first
step: W=(dV)^WESP.
SHLIM: limit for shifts in BSTAC4 and FBSTAC4 (if SHLIM=0 no limit)
(not used in STACO4 and FSTACO4)

3) (NC times)
COMP
COMP
COMP: name of mass balance equation

4) TEMP,PHI,PHF
Expand Down Expand Up @@ -126,7 +126,7 @@ goto item 10
BLOG: log(BETA)
IB: reference ionic strenght (to be given only if IREF<0)
C,D,E: parameters of Debye-Huckel equation
(if C=D=E=0 then:
(if C=D=E=0 then:
C= c0 p* + c1 z*
D= d0 p* + d1 z*
E= e0 p* + e1 z* )
Expand Down Expand Up @@ -156,7 +156,7 @@ goto item 10
refers to the component NCET

12) (NC times)
CO,CTT,LOK
CO,CTT,LOK
CO: initial concentration in the titration vessel (mol/L)
CTT: concentration in the titrant (mol/L)
LOK = 0: CO constant
Expand Down Expand Up @@ -191,7 +191,7 @@ goto item 10
= 1: JB refined
LOK4 = 0: SLOPE constant
= 1: SLOPE refined

16) V,E,(SIGMA),IND
V: titrant volume
E: potential (or pH, if EO=0)
Expand All @@ -214,4 +214,3 @@ goto item 10
(**) STACO4, FSTACO4: the same parameters must be constrained
for all the titrations
BSTAC4, FBSTAC4: one can constrain several groups of parameters

87 changes: 1 addition & 86 deletions notebooks/test_bstac_import.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -235,96 +235,11 @@
" result[name] = parsed_section\n",
" line_counter += ns\n",
" elif repeat == \"end_of_file\":\n",
" parsed_section = process_func(\n",
" lines[line_counter:], result[\"JW\"], nc\n",
" )\n",
" parsed_section = process_func(lines[line_counter:], result[\"JW\"], nc)\n",
" result[name] = parsed_section\n",
"\n",
" return result"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from libeq.parsers.bstac import parse_file\n",
"\n",
"with open(\"/Users/lorenzo/Coding/libeq/notebooks/Zn-EDTA\", \"r\") as file:\n",
" lines = file.readlines()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"res = parse_file(lines)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'C0': 0.001944, 'CTT': 0.0, 'LOK': 0},\n",
" {'C0': 0.001988, 'CTT': 0.0, 'LOK': 1},\n",
" {'C0': 0.028132, 'CTT': -0.2009, 'LOK': 1}]"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res[\"titrations\"][0][\"components_concentrations\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"# your list of dictionaries\n",
"ix_values = [[d[key] for key in d if key.startswith('IX')] for d in res[\"species\"]]"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[ 0, 1, 1, 1, 1, 2, 2, 0, 0, 0, 0, 0, 0, 1, 1, 1],\n",
" [ 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n",
" [-1, -1, -2, -3, -4, -1, -6, 1, 2, 3, 4, 5, 6, 0, 1, -1]])"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import numpy as np\n",
"np.array(ix_values).T"
]
}
],
"metadata": {
Expand Down
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