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Identical blocks of code found in 2 locations. Consider refactoring.
Open

        for i in range(2, 6):
            particle = self.system.storage.getParticle(i)
            mass.append(particle.mass)
            diff = []
            for j in range(3):
Severity: Major
Found in testsuite/constrain_com/testCaseConstrainCOM.py and 1 other location - About 1 day to fix
testsuite/constrain_com/testCaseConstrainCOM.py on lines 138..146

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 162.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        for i in range(2, 6):
            particle = self.system.storage.getParticle(i)
            mass.append(particle.mass)
            diff = []
            for j in range(3):
Severity: Major
Found in testsuite/constrain_com/testCaseConstrainCOM.py and 1 other location - About 1 day to fix
testsuite/constrain_com/testCaseConstrainCOM.py on lines 106..114

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 162.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/adress/fadress_tetraliquid/adress.py and 1 other location - About 1 day to fix
examples/convert_gromacs_tables/convert_gromacs_table.py on lines 71..84

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 161.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/convert_gromacs_tables/convert_gromacs_table.py and 1 other location - About 1 day to fix
examples/adress/fadress_tetraliquid/adress.py on lines 52..66

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 161.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        particle_list = [
            (1, 1, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
            (2, 1, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
            (3, 1, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 0),
            (4, 1, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 45..55
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 186..196

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 156.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        particle_list = [
            (1, 1, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
            (2, 1, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
            (3, 1, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 0),
            (4, 1, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 45..55
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 116..126

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 156.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        particle_list = [
            (1,  1, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
            (2,  1, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
            (3,  1, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 0),
            (4,  1, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 116..126
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 186..196

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 156.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

for j in range(0, num_particles):
    print((format2 % (j, ' ', \
                         system.storage.getParticle(j).f.x, ' ', \
                         system.storage.getParticle(j).f.y, ' ', \
                         system.storage.getParticle(j).f.z, \
Severity: Major
Found in examples/ewald/ewald.py and 1 other location - About 1 day to fix
testsuite/ewald/ewald_eppDeserno_comparison.py on lines 176..184

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 154.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

for j in range(0, num_particles):
    print((format2 % (j, ' ', \
                         system.storage.getParticle(j).f.x, ' ', \
                         system.storage.getParticle(j).f.y, ' ', \
                         system.storage.getParticle(j).f.z, \
Severity: Major
Found in testsuite/ewald/ewald_eppDeserno_comparison.py and 1 other location - About 1 day to fix
examples/ewald/ewald.py on lines 177..185

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 154.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Function read_charmm has a Cognitive Complexity of 67 (exceeds 5 allowed). Consider refactoring.
Open

def read_charmm(fin):

    f = open(fin)
    line = f.readline() # comment line
    while not 'atoms' in line: #skip possible blank line
Severity: Minor
Found in src/tools/lammps.py - About 1 day to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        if int(defaults['combinationrule'])==1:
            for atnr, at in atomtypeparams.items():
                c6=float(at['sig'])
                c12=float(at['eps'])
                if c6==0: continue
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
src/tools/gromacs.py on lines 1152..1162

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 151.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    if defaults:
        if int(defaults['combinationrule'])==1:
            for atnr, at in atomtypeparams.items():
                c6=float(at['sig'])
                c12=float(at['eps'])
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
src/tools/gromacs.py on lines 1190..1199

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 151.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        for i in range(2, 6):
            particle = self.system.storage.getParticle(i)
            diff = []
            for j in range(3):
                x_i = particle.pos[j] - dmy_p[i - 2][j]
Severity: Major
Found in testsuite/constrain_rg/testCaseConstrainRG.py and 1 other location - About 1 day to fix
testsuite/constrain_rg/testCaseConstrainRG.py on lines 134..141

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 151.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        for i in range(2, 6):
            particle = self.system.storage.getParticle(i)
            diff = []
            for j in range(3):
                x_i = particle.pos[j] - dmy_p[i - 2][j]
Severity: Major
Found in testsuite/constrain_rg/testCaseConstrainRG.py and 1 other location - About 1 day to fix
testsuite/constrain_rg/testCaseConstrainRG.py on lines 101..108

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 151.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

                            boxList = [(1 - slabMSDims[0]) * box_size[0] * (pow(ratioMS, 0.3333)) + boxList[0], (1 - slabMSDims[1]) * box_size[1] * (pow(ratioMS, 0.3333)) + boxList[1], (1 - slabMSDims[2]) * box_size[2] * (pow(ratioMS, 0.3333)) + boxList[2]]
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 1 day to fix
src/tools/decomp.py on lines 139..139

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 150.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

                        boxList = [(1 - slabMSDims[0]) * box_size[0] * (pow(ratioMS, 0.3333)) + boxList[0], (1 - slabMSDims[1]) * box_size[1] * (pow(ratioMS, 0.3333)) + boxList[1], (1 - slabMSDims[2]) * box_size[2] * (pow(ratioMS, 0.3333)) + boxList[2]]  # Flag NOR
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 1 day to fix
src/tools/decomp.py on lines 157..157

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 150.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    for idcla, idpi in ringids.items():
        p=allParticlesById[idcla]
        mass=p[propDict['mass']]
        interactionList=kineticTermInteractions[mass].getFixedPairList() #find the appropriate interaction based on the mass
        # harmonic spring between atom at imag-time i and imag-time i+1
Severity: Major
Found in src/tools/pathintegral.py and 1 other location - About 1 day to fix
testsuite/pi_water/pathintegral.py on lines 143..152

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 146.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    for idcla, idpi in ringids.items():
        p=allParticlesById[idcla]
        mass=p[propDict['mass']]
        interactionList=kineticTermInteractions[mass].getFixedPairList() #find the appropriate interaction based on the mass
        # harmonic spring between atom at imag-time i and imag-time i+1
Severity: Major
Found in testsuite/pi_water/pathintegral.py and 1 other location - About 1 day to fix
src/tools/pathintegral.py on lines 267..276

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 146.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 2 locations. Consider refactoring.
Open

    if(num_angles != 0):
        # find and store angle coeff
        line = ''
        while not 'Angle Coeffs' in line:
            line = f.readline()
Severity: Major
Found in src/tools/lammps.py and 1 other location - About 1 day to fix
src/tools/lammps.py on lines 259..273

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 141.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

        for i in range (halo, myNi[0]-halo):
            for j in range (halo, myNi[1]-halo):
                for k in range (halo, myNi[2]-halo):
                    av_den += self.lb.getLBMom(Int3D(i,j,k), 0)
Severity: Major
Found in testsuite/lattice_boltzmann/test_extForce.py and 1 other location - About 1 day to fix
testsuite/lattice_boltzmann/test_LatticeBoltzmann.py on lines 93..100

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 141.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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