Why do I get a "view" error:
ndf = pd.DataFrame()
ndf['Signals'] = [1,1,1,1,1,0,0,0,0,0]
signals_diff = ndf.Signals.diff()
ndf['Revals'] = [101,102,105,104,105,106,107,108,109,109]
ndf['Entry'] = 0
for i,element in enumerate(signals_diff):
if (i==0):
ndf.iloc[i]['Entry'] = ndf.iloc[i]['Revals']
elif (element == 0):
ndf.iloc[i]['Entry'] = ndf.iloc[i - 1]['Entry']
else:
ndf.iloc[i]['Entry'] = ndf.iloc[i]['Revals']
A value is trying to be set on a copy of a slice from a DataFrame
See the caveats in the documentation:
https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
ndf.iloc[i]['Entry'] = ndf.iloc[i]['Revals']
instead of iloc use loc:
ndf = pd.DataFrame()
ndf['Signals'] = [1,1,1,1,1,0,0,0,0,0]
signals_diff = ndf.Signals.diff()
ndf['Revals'] = [101,102,105,104,105,106,107,108,109,109]
ndf['Entry'] = 0
for i,element in enumerate(signals_diff):
if (i==0):
ndf.loc[i,'Entry'] = ndf.loc[i,'Revals']
elif (element == 0):
ndf.loc[i,'Entry'] = ndf.loc[i - 1,'Entry']
else:
ndf.loc[i,'Entry'] = ndf.loc[i,'Revals']
This will solve the problem but when assigning, the index should be same. So because of the index thing you might not be able to get the expected result.
Do not chain indexes like ndf.iloc[i]['Entry'] when trying to assign something. See why does that not work.
That said, your code can be rewrite as:
ndf['Entry'] = ndf['Revals'].where(signals_diff != 0).ffill()
Output:
Signals Revals Entry
0 1 101 101.0
1 1 102 101.0
2 1 105 101.0
3 1 104 101.0
4 1 105 101.0
5 0 106 106.0
6 0 107 106.0
7 0 108 106.0
8 0 109 106.0
9 0 109 106.0
Let us keep using the index position slice with get_indexer
for i,element in enumerate(signals_diff):
if (i==0):
ndf.iloc[i,ndf.columns.get_indexer(['Entry'])] = ndf.iloc[i,ndf.columns.get_indexer(['Revals'])]
elif (element == 0):
ndf.iloc[i,ndf.columns.get_indexer(['Entry'])] = ndf.iloc[i - 1,ndf.columns.get_indexer(['Entry'])]
else:
ndf.iloc[i,ndf.columns.get_indexer(['Entry'])] = ndf.iloc[i,ndf.columns.get_indexer(['Revals'])]
I want to solve a continuum mechanics problem thanks to FEniCS. I apply pressure and take into account the weight. But when I add the thermoelasticity component, it doesn't work anymore.
Here is my code :
from dolfin import *
from fenics import *
from ufl import nabla_div
from ufl import as_tensor
import matplotlib.pyplot as plt
import numpy as np
E = Constant(100*10**9)
nu = Constant(0.3)
Lg = 0.01; W = 0.2
mu = E/(2+2*nu)
rho = Constant(2200)
delta = W/Lg
gamma = 0.4*delta**2
beta = 8
lambda_ = (E*nu)/((1+nu)*(1-2*nu))
alpha = 1.2*(10**(-8))
deltaT = Constant(50)
Kt = E*alph*deltaT/(1-2*nu)
g = 9.81
tol = 1E-14
# Create mesh and define function space
mesh = RectangleMesh(Point(-2., 0.),Point(2., 10.), 80, 200)
V = VectorFunctionSpace(mesh, "P", 1)
# Define boundary condition
def clamped_boundary(x, on_boundary):
return on_boundary and x[1] < tol
class UpFace(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and (x[1] > 10 - tol)
ueN = UpFace()
boundaries = MeshFunction("size_t", mesh, mesh.topology().dim()-1, 0)
ueN.mark(boundaries, 1)
ds = Measure("ds", domain=mesh, subdomain_data=boundaries)
bc = DirichletBC(V, Constant((0, 0)), clamped_boundary)
def epsilon(u):
return 0.5*(nabla_grad(u) + nabla_grad(u).T)
def sigma(u):
return (lambda_*nabla_div(u) - Kt)*Identity(d) + (2*mu)*epsilon(u)
# Define variational problem
u = TrialFunction(V)
d = u.geometric_dimension() # space dimension
v = TestFunction(V)
f = Constant((0,-rho*g))
T = Constant((0, 0))
Pr = Constant((0, -2*10**9))
a = inner(sigma(u), epsilon(v))*dx
L = dot(f, v)*dx + dot(T, v)*ds + dot(Pr,v)*ds(1)
# Compute solution
u = Function(V)
solve(a == L, u, bc)
# Plot solution
plot(u, mode="displacement", color= "red")
plt.colorbar(plot(u))
I get this error message :
---------------------------------------------------------------------------
ArityMismatch Traceback (most recent call last)
<ipython-input-54-805d7c5b704f> in <module>
17 # Compute solution
18 u = Function(V)
---> 19 solve(a == L, u, bc)
20
21 # Plot solution
/usr/lib/python3/dist-packages/dolfin/fem/solving.py in solve(*args, **kwargs)
218 # tolerance)
219 elif isinstance(args[0], ufl.classes.Equation):
--> 220 _solve_varproblem(*args, **kwargs)
221
222 # Default case, just call the wrapped C++ solve function
/usr/lib/python3/dist-packages/dolfin/fem/solving.py in _solve_varproblem(*args, **kwargs)
240 # Create problem
241 problem = LinearVariationalProblem(eq.lhs, eq.rhs, u, bcs,
--> 242 form_compiler_parameters=form_compiler_parameters)
243
244 # Create solver and call solve
/usr/lib/python3/dist-packages/dolfin/fem/problem.py in __init__(self, a, L, u, bcs, form_compiler_parameters)
54 else:
55 L = Form(L, form_compiler_parameters=form_compiler_parameters)
---> 56 a = Form(a, form_compiler_parameters=form_compiler_parameters)
57
58 # Initialize C++ base class
/usr/lib/python3/dist-packages/dolfin/fem/form.py in __init__(self, form, **kwargs)
42
43 ufc_form = ffc_jit(form, form_compiler_parameters=form_compiler_parameters,
---> 44 mpi_comm=mesh.mpi_comm())
45 ufc_form = cpp.fem.make_ufc_form(ufc_form[0])
46
/usr/lib/python3/dist-packages/dolfin/jit/jit.py in mpi_jit(*args, **kwargs)
45 # Just call JIT compiler when running in serial
46 if MPI.size(mpi_comm) == 1:
---> 47 return local_jit(*args, **kwargs)
48
49 # Default status (0 == ok, 1 == fail)
/usr/lib/python3/dist-packages/dolfin/jit/jit.py in ffc_jit(ufl_form, form_compiler_parameters)
95 p.update(dict(parameters["form_compiler"]))
96 p.update(form_compiler_parameters or {})
---> 97 return ffc.jit(ufl_form, parameters=p)
98
99
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit(ufl_object, parameters, indirect)
215
216 # Inspect cache and generate+build if necessary
--> 217 module = jit_build(ufl_object, module_name, parameters)
218
219 # Raise exception on failure to build or import module
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit_build(ufl_object, module_name, parameters)
131 name=module_name,
132 params=params,
--> 133 generate=jit_generate)
134 return module
135
/usr/lib/python3/dist-packages/dijitso/jit.py in jit(jitable, name, params, generate, send, receive, wait)
163 elif generate:
164 # 1) Generate source code
--> 165 header, source, dependencies = generate(jitable, name, signature, params["generator"])
166 # Ensure we got unicode from generate
167 header = as_unicode(header)
/usr/lib/python3/dist-packages/ffc/jitcompiler.py in jit_generate(ufl_object, module_name, signature, parameters)
64
65 code_h, code_c, dependent_ufl_objects = compile_object(ufl_object,
---> 66 prefix=module_name, parameters=parameters, jit=True)
67
68 # Jit compile dependent objects separately,
/usr/lib/python3/dist-packages/ffc/compiler.py in compile_form(forms, object_names, prefix, parameters, jit)
141 """This function generates UFC code for a given UFL form or list of UFL forms."""
142 return compile_ufl_objects(forms, "form", object_names,
--> 143 prefix, parameters, jit)
144
145
/usr/lib/python3/dist-packages/ffc/compiler.py in compile_ufl_objects(ufl_objects, kind, object_names, prefix, parameters, jit)
183 # Stage 1: analysis
184 cpu_time = time()
--> 185 analysis = analyze_ufl_objects(ufl_objects, kind, parameters)
186 _print_timing(1, time() - cpu_time)
187
/usr/lib/python3/dist-packages/ffc/analysis.py in analyze_ufl_objects(ufl_objects, kind, parameters)
88 # Analyze forms
89 form_datas = tuple(_analyze_form(form, parameters)
---> 90 for form in forms)
91
92 # Extract unique elements accross all forms
/usr/lib/python3/dist-packages/ffc/analysis.py in <genexpr>(.0)
88 # Analyze forms
89 form_datas = tuple(_analyze_form(form, parameters)
---> 90 for form in forms)
91
92 # Extract unique elements accross all forms
/usr/lib/python3/dist-packages/ffc/analysis.py in _analyze_form(form, parameters)
172 do_apply_geometry_lowering=True,
173 preserve_geometry_types=(Jacobian,),
--> 174 do_apply_restrictions=True)
175 elif r == "tsfc":
176 try:
/usr/lib/python3/dist-packages/ufl/algorithms/compute_form_data.py in compute_form_data(form, do_apply_function_pullbacks, do_apply_integral_scaling, do_apply_geometry_lowering, preserve_geometry_types, do_apply_default_restrictions, do_apply_restrictions, do_estimate_degrees, do_append_everywhere_integrals, complex_mode)
416 preprocessed_form = remove_complex_nodes(preprocessed_form)
417
--> 418 check_form_arity(preprocessed_form, self.original_form.arguments(), complex_mode) # Currently testing how fast this is
419
420 # TODO: This member is used by unit tests, change the tests to
/usr/lib/python3/dist-packages/ufl/algorithms/check_arities.py in check_form_arity(form, arguments, complex_mode)
175 def check_form_arity(form, arguments, complex_mode=False):
176 for itg in form.integrals():
--> 177 check_integrand_arity(itg.integrand(), arguments, complex_mode)
/usr/lib/python3/dist-packages/ufl/algorithms/check_arities.py in check_integrand_arity(expr, arguments, complex_mode)
157 key=lambda x: (x.number(), x.part())))
158 rules = ArityChecker(arguments)
--> 159 arg_tuples = map_expr_dag(rules, expr, compress=False)
160 args = tuple(a[0] for a in arg_tuples)
161 if args != arguments:
/usr/lib/python3/dist-packages/ufl/corealg/map_dag.py in map_expr_dag(function, expression, compress)
35 Return the result of the final function call.
36 """
---> 37 result, = map_expr_dags(function, [expression], compress=compress)
38 return result
39
/usr/lib/python3/dist-packages/ufl/corealg/map_dag.py in map_expr_dags(function, expressions, compress)
84 r = handlers[v._ufl_typecode_](v)
85 else:
---> 86 r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands])
87
88 # Optionally check if r is in rcache, a memory optimization
/usr/lib/python3/dist-packages/ufl/algorithms/check_arities.py in sum(self, o, a, b)
46 def sum(self, o, a, b):
47 if a != b:
---> 48 raise ArityMismatch("Adding expressions with non-matching form arguments {0} vs {1}.".format(_afmt(a), _afmt(b)))
49 return a
50
ArityMismatch: Adding expressions with non-matching form arguments () vs ('v_1',).
When I write this (I remove the Kt from sigma(u)):
def sigma(u):
return (lambda_*nabla_div(u))*Identity(d) + (2*mu)*epsilon(u)
It works perfectly.
In this page (Click here), they try to plot the same kind problem and it works on my computer.
Do you know how to fix it ?
I had exactly the same question and a colleague of mine did figure it out for me. As there is no answer given here, I will try to leave some directions to guide others to the solution. I have not a lot of expertise yet, so please consider that my use of terminology might be a little bit off.
The error of fenics somewhat mislead me into thinking the error is in the definition of the stress term sigma. It is not exactly there. The right handside and the left handside in the solve function are not defined correctly (also shown in the very top of the error code). The term kT*Identity(d) in the stress function sigma, is not dependent on the trialfunction u. It is just multiplied by the testfunction v later (epsilon(v)). Therefore it has to go into the L of the equation of the solver.
Beneath the Link that you shared, the scipt uses the rhs and lhs function to correctly split the equation into a and L.
I try to call a callback function in cython cdef block, I can printf the actual data during cython function call, but when my callback function was called or I call a print(buffer) in cython cdef block, I got the (paramter/result) with b'',I try other demo, It's all works fine.
windows 10, python3.7, cython
cython block
cdef ikcp_output(self, char *buffer, int size):
print("size: {}".format(size)) this can work
for i in range(size):
print(buffer[i]) # this can also works
cdef char* o
o = <char*> malloc(sizeof(char) * size)
memcpy(o, buffer, size)
for i in range(size):
print(o[i]) # this can also works
print(o) # this output b''
self.output(o) # the callback function get a parameter b''
free(o)
start iter buffer
0
0
0
1
81
0
0
32
28
-50
-113
-50
0
0
0
0
0
0
0
0
49
50
49
51
50
49
51
49
51
49
50
10
start iter o
0
0
0
1
81
0
0
32
28
-50
-113
-50
0
0
0
0
0
0
0
0
49
50
49
51
50
49
51
49
51
49
50
10
32
b'' # this is what i got in callback function
client output
output data b'' to addr: ('127.0.0.1', 8888)
Calling either print(o) or self.func(o) involves converting o to a Python object, in this case a bytes object. This conversion assumes that the char* is a c string (i.e. is null terminated) since Cython has no other way to determine the length. However your buffer starts with 0, and so is read a 0-length string.
The correct solution is to do the conversion manually using PyBytes_FromStringAndSize. You pass this a char* and the length of the string (hence it doesn't assume that the first 0 is the end of the string). You can cimport it from cpython.bytes.
Sort the given set of numbers using Bubble Sort. The first line of the input contains the number of elements, the second line of the input contains the numbers to be sorted. In the output print the status of the array at the 3rd iteration and the final sorted array in the given format
alist=[]
def bubble_sort(alist):
for i in range(len(alist) - 1, 0, -1):
no_swap = True
for j in range(0, i):
if alist[j + 1] < alist[j]:
alist[j], alist[j + 1] = alist[j + 1], alist[j]
no_swap = False
if no_swap:
return
n=int(input())
for i in range(n):
alist.append(int(input()))
alist = [int(x) for x in alist]
bubble_sort(alist)
print('Sorted array: ', end='\n')
for i in alist:
print(i,end=" ")
Test Case 1
7
64
34
25
12
22
11
90
Expected Output:
It should print the following 3 lines
12 22 11 25 34 64 90
Sorted array:
11 12 22 25 34 64 90
Test Case 2
8
14
83
25
47
9
77
1
0
Expected Output:
It should print the 3 following lines
14 9 25 1 0 47 77 83
Sorted array:
0 1 9 14 25 47 77 83
Just add in your for loop a print when you reach the third iteration
alist=[]
def bubble_sort(alist):
number_of_iterations = 0
for i in range(len(alist) - 1, 0, -1):
no_swap = True
for j in range(0, i):
if alist[j + 1] < alist[j]:
alist[j], alist[j + 1] = alist[j + 1], alist[j]
no_swap = False
if i == len(alist) - 3:
print(*alist) # Using the unpacking operator for pretty print, if you are in python2 you can print it this way : " ".join(map(str, alist))
if no_swap:
return
n=5
alist = [7, 64, 34, 25, 12, 22, 11, 90]
bubble_sort(alist)
print('Sorted array: ', end='\n')
for i in alist:
print(i,end=" ")
I am reading a text file using python. Each line will be read if the first character does not equal to # or #. The content of the text is pasted in the end.
This works:
if line[0] != '#' and line[0] != '#':
value=float(line[3:8])
But this does not work:
if line[0] != ('#' and '#'):
value=float(line[3:8])
ValueError: could not convert string to float: 'his f'
This also does not work:
if line[0] != ('#' or '#'):
value=float(line[3:8])
ValueError: could not convert string to float: ' tit'
So why both or and and not work?
The content of the text file:
# This file was created Wed Feb 21 12:32:25 2018
# Created by:
# :-) GROMACS - gmx do_dssp, VERSION 5.1.1 (-:
#
# Executable: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2/bin//gmx
# Data prefix: /shared/ucl/apps/gromacs/5.1.1/intel-2015-update2
# Command line:
# gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
# gmx do_dssp is part of G R O M A C S:
#
# Gnomes, ROck Monsters And Chili Sauce
#
# title "Secondary Structure"
# xaxis label "Time (ns)"
# yaxis label "Number of Residues"
#TYPE xy
# subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn"
# view 0.15, 0.15, 0.75, 0.85
# legend on
# legend box on
# legend loctype view
# legend 0.78, 0.8
# legend length 2
# s0 legend "Structure"
# s1 legend "Coil"
# s2 legend "B-Sheet"
# s3 legend "B-Bridge"
# s4 legend "Bend"
# s5 legend "Turn"
# s6 legend "A-Helix"
# s7 legend "3-Helix"
# s8 legend "5-Helix"
0 278 106 199 10 44 60 9 15 0
0.1 267 118 203 7 52 47 10 6 0
0.2 245 144 175 8 54 51 11 0 0
0.3 264 118 192 8 58 56 8 3 0
line[0] not in ['#' , '#'] will do the trick.
It checks if line[0] exists in a given array.