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

            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)

                    jx = self.lb.getLBMom(Int3D(i,j,k), 1)
Severity: Major
Found in testsuite/lattice_boltzmann/test_LatticeBoltzmann.py and 1 other location - About 1 day to fix
testsuite/lattice_boltzmann/test_extForce.py on lines 75..83

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

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

    if(num_bonds != 0):
        # find and store bond coeff
        line = ''
        while not 'Bond 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 290..304

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

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

        if flz == 0:
            halfneilListz = halfDecomp(adrCenter[2], rc_skin, eh_size, int(round(node_grid[2] / 2. - 0.5)), cellsZ, ratioMS, cursor[2], idealGasFlag)
            print("HeSpaDDA message: My halfneilListx called a half decomposition of the first half of the sim box as (algorithm S.1)...,", halfneilListz)
            neiListzin = addHsymmetry(halfneilListz, eh_size, rc_skin, node_grid[2], cellsZ, ratioMS, cursor[2], idealGasFlag)
            print("HeSpaDDA message: My neiListxin if it make sense your heterogenous system can be splitted in 2 equal parts (algorithm S.2)...,", neiListzin)
Severity: Major
Found in src/tools/decomp.py and 2 other locations - About 1 day to fix
src/tools/decomp.py on lines 478..484
src/tools/decomp.py on lines 487..493

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 139.

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

        if flx == 0:
            halfneilListx = halfDecomp(adrCenter[0], rc_skin, eh_size, int(round(node_grid[0] / 2. - 0.5)), cellsX, ratioMS, cursor[0], idealGasFlag)
            print("HeSpaDDA message: My halfneilListx called a half decomposition of the first half of the sim box as (algorithm S.1)...,", halfneilListx)
            neiListxin = addHsymmetry(halfneilListx, eh_size, rc_skin, node_grid[0], cellsX, ratioMS, cursor[0], idealGasFlag)
            print("HeSpaDDA message: My neiListxin if it make sense your heterogenous system can be splitted in 2 equal parts (algorithm S.2)...,", neiListxin)
Severity: Major
Found in src/tools/decomp.py and 2 other locations - About 1 day to fix
src/tools/decomp.py on lines 487..493
src/tools/decomp.py on lines 496..502

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 139.

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

        if fly == 0:
            halfneilListy = halfDecomp(adrCenter[1], rc_skin, eh_size, int(round(node_grid[1] / 2. - 0.5)), cellsY, ratioMS, cursor[1], idealGasFlag)
            print("HeSpaDDA message: My halfneilListx called a half decomposition of the first half of the sim box as (algorithm S.1)...,", halfneilListy)
            neiListyin = addHsymmetry(halfneilListy, eh_size, rc_skin, node_grid[1], cellsY, ratioMS, cursor[1], idealGasFlag)
            print("HeSpaDDA message: My neiListxin if it make sense your heterogenous system can be splitted in 2 equal parts (algorithm S.2)...,", neiListyin)
Severity: Major
Found in src/tools/decomp.py and 2 other locations - About 1 day to fix
src/tools/decomp.py on lines 478..484
src/tools/decomp.py on lines 496..502

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 139.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        # set up system
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        # set up system
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):

        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/rattle/testRattle.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        # set up system
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/AdResS/AdressDensity/test_AdressDensity.py and 6 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
        system.skin = 0.3
Severity: Major
Found in testsuite/thermo_integration/testThermoIntegration.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        # set up system
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/AdResS/HAdResS/test_HAdResS.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 7 locations. Consider refactoring.
Open

    def setUp(self):
        # set up system
        system = espressopp.System()
        box = (10, 10, 10)
        system.bc = espressopp.bc.OrthorhombicBC(system.rng, box)
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 6 other locations - About 1 day to fix
testsuite/AdResS/AdressDensity/test_AdressDensity.py on lines 31..41
testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py on lines 32..42
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 31..41
testsuite/AdResS/TDforce/test_TDforce.py on lines 31..41
testsuite/rattle/testRattle.py on lines 36..46
testsuite/thermo_integration/testThermoIntegration.py on lines 31..40

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 138.

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 polymerRW has a Cognitive Complexity of 58 (exceeds 5 allowed). Consider refactoring.
Open

def polymerRW(pid, startpos, numberOfMonomers, bondlength, return_angles=False, return_dihedrals=False, mindist=None, rng=None):
    """
    Initializes polymers through random walk
    """
Severity: Minor
Found in src/tools/topology.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

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

        if slabMSDims[1] == 1:
            halfneilListy = halfDecomp(adrCenter[1], rc_skin, eh_size, int(round(node_grid[1] / 2. - 0.5)), cellsY, ratioMS, cursor[1], idealGasFlag)
            print("HeSpaDDA message: My halfneilListx called a half decomposition of the first half of the sim box as (algorithm S.1)...,", halfneilListy)
            # Next instruction is doubling(by unfolding halfDecomp) the halfspace based DD
            neiListyin = addHsymmetry(halfneilListy, eh_size, rc_skin, node_grid[1], cellsY, ratioMS, cursor[1], idealGasFlag)
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 1 day to fix
src/tools/decomp.py on lines 463..470

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 135.

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 slabMSDims[2] == 1:
            halfneilListz = halfDecomp(adrCenter[2], rc_skin, eh_size, int(round(node_grid[2] / 2. - 0.5)), cellsZ, ratioMS, cursor[2], idealGasFlag)
            print("HeSpaDDA message: My halfneilListx called a half decomposition of the first half of the sim box as (algorithm S.1)...,", halfneilListz)
            # Next instruction is doubling(by unfolding halfDecomp) the halfspace based DD
            neiListzin = addHsymmetry(halfneilListz, eh_size, rc_skin, node_grid[2], cellsZ, ratioMS, cursor[2], idealGasFlag)
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 1 day to fix
src/tools/decomp.py on lines 453..460

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 135.

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 write has a Cognitive Complexity of 57 (exceeds 5 allowed). Consider refactoring.
Open

def write(fileName, system, folded=True, writeVelocities=False):

    # first collect all the information that we need to write into the file
    numParticles  = int(espressopp.analysis.NPart(system).compute())
    box_x = system.bc.boxL[0]
Severity: Minor
Found in src/tools/io_extended.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

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

        for i in range(N):
            for j in range(N):
                for k in range(N):

                    r = 0.25
Severity: Major
Found in testsuite/FixedLocalTuple/testFixedLocalTupleList.py and 2 other locations - About 1 day to fix
testsuite/FixedLocalTuple/testFixedLocalTupleList.py on lines 65..76
testsuite/unittest/testVerletList.py on lines 72..83

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 133.

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

        for i in range(N):
            for j in range(N):
                for k in range(N):

                    r = 0.5
Severity: Major
Found in testsuite/unittest/testVerletList.py and 2 other locations - About 1 day to fix
testsuite/FixedLocalTuple/testFixedLocalTupleList.py on lines 65..76
testsuite/FixedLocalTuple/testFixedLocalTupleList.py on lines 78..89

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 133.

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

        for i in range(N):
            for j in range(N):
                for k in range(N):

                    r = 0.5
Severity: Major
Found in testsuite/FixedLocalTuple/testFixedLocalTupleList.py and 2 other locations - About 1 day to fix
testsuite/FixedLocalTuple/testFixedLocalTupleList.py on lines 78..89
testsuite/unittest/testVerletList.py on lines 72..83

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 133.

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 pid_trotter in range(nTrotter):
                pid = pid_atom*nTrotter+pid_trotter
                allParticles.append([(allParticlesAT[pid])[0],
                                    (allParticlesAT[pid])[1], (allParticlesAT[pid])[2], (allParticlesAT[pid])[3], (allParticlesAT[pid])[4],
                                    (allParticlesAT[pid])[5], (allParticlesAT[pid])[6], (allParticlesAT[pid])[7]])
Severity: Major
Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 day to fix
examples/adress/piadress_water/AdaptivePIwater.py on lines 165..174

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 132.

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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