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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

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(int(nTrotter)):
        pid = pid_atom*nTrotter+pid_trotter
        allParticles.append([(allParticlesAT[pid])[0],
                            (allParticlesAT[pid])[1], # pos
                            (allParticlesAT[pid])[2], # vel
Severity: Major
Found in examples/adress/piadress_water/AdaptivePIwater.py and 1 other location - About 1 day to fix
testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 132..136

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

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

    def test3Properties(self) :
        'Test Real3D properties.'
        v = Real3D(1.0, 2.0, 3.0)
        self.assertEqual(v.x, 1.0)
        self.assertEqual(v.y, 2.0)
Severity: Major
Found in testsuite/unittest/testReal3D.py and 1 other location - About 1 day to fix
testsuite/unittest/testInt3D.py on lines 74..87

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

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

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

    def test3Properties(self) :
        'Test Int3D properties.'
        v = Int3D(1, 2, 3)
        self.assertEqual(v.x, 1)
        self.assertEqual(v.y, 2)
Severity: Major
Found in testsuite/unittest/testInt3D.py and 1 other location - About 1 day to fix
testsuite/unittest/testReal3D.py on lines 79..92

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

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

def setDihedralInteractionsAdress(system, dihedrals, dihedraltypeparams, ftpl):
    dihedral_interactions = {}

    for idlist, dihedrallist in dihedrals.items():
        fpl = espressopp.FixedQuadrupleListAdress(system.storage, ftpl)
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
src/tools/gromacs.py on lines 1065..1080

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 131.

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

        elif totNodesEH % 2 != 0 and totCellsEH % 2 != 0:
            [wholeNeiListX_EH.append(round(totCellsEH / totNodesEH - 0.5)) for i in range(totNodesEH)]
            if int(totCellsEH - sum(wholeNeiListX_EH)) != 0:
                wholeNeiListX_EH[0:totNodesEH] = redistDeltaRandomly(wholeNeiListX_EH[0:totNodesEH], totCellsEH - sum(wholeNeiListX_EH[0:totNodesEH]), 0)
            else:
Severity: Major
Found in src/tools/loadbal.py and 1 other location - About 1 day to fix
src/tools/loadbal.py on lines 369..375

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 131.

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

        elif totNodesCG % 2 != 0 and totCellsCG % 2 != 0:
            [wholeNeiListX_CG.append(round(totCellsCG / totNodesCG - 0.5)) for i in range(totNodesCG)]
            if int(totCellsCG - sum(wholeNeiListX_CG)) != 0:
                wholeNeiListX_CG[0:totNodesCG] = redistDeltaRandomly(wholeNeiListX_CG[0:totNodesCG], totCellsCG - sum(wholeNeiListX_CG[0:totNodesCG]), 0)
            else:
Severity: Major
Found in src/tools/loadbal.py and 1 other location - About 1 day to fix
src/tools/loadbal.py on lines 347..353

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 131.

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

def setImproperInteractionsAdress(system, impropers, impropertypeparams, ftpl):
    improper_interactions = {}

    for idlist, improperlist in impropers.items():
        fpl = espressopp.FixedQuadrupleListAdress(system.storage, ftpl)
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
src/tools/gromacs.py on lines 1047..1062

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 131.

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

Severity: Major
Found in testsuite/interaction_potentials/unittest/testFENE.py and 1 other location - About 1 day to fix
testsuite/interaction_potentials/unittest/testMorse.py on lines 0..35

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 130.

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

Severity: Major
Found in testsuite/interaction_potentials/unittest/testMorse.py and 1 other location - About 1 day to fix
testsuite/interaction_potentials/unittest/testFENE.py on lines 0..37

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 130.

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(velocities):
        # find and store velocities
        line = ''
        while not 'Velocities' 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 351..364

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 125.

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(velocities):
        # find and store velocities
        line = ''
        while not 'Velocities' 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 126..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 125.

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 3 locations. Consider refactoring.
Open

for i in range(3):
    line = input_file.readline()
    parameters = line.split()
    if parameters[0] == "num_chains:":
        num_chains = int(parameters[1])
Severity: Major
Found in examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py and 2 other locations - About 7 hrs to fix
examples/hierarchical_strategy_for_one-component/generate_microscopic-c.py on lines 20..28
examples/hierarchical_strategy_for_one-component/reinsertion.py on lines 24..32

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 121.

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 3 locations. Consider refactoring.
Open

for i in range(3):
    line = input_file.readline()
    parameters = line.split()
    if parameters[0] == "num_chains:":
        num_chains = int(parameters[1])
Severity: Major
Found in examples/hierarchical_strategy_for_one-component/generate_microscopic-c.py and 2 other locations - About 7 hrs to fix
examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py on lines 19..27
examples/hierarchical_strategy_for_one-component/reinsertion.py on lines 24..32

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 121.

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 3 locations. Consider refactoring.
Open

for i in range(3):
    line = input_file.readline()
    parameters = line.split()
    if parameters[0] == "num_chains:":
        num_chains = int(parameters[1])
Severity: Major
Found in examples/hierarchical_strategy_for_one-component/reinsertion.py and 2 other locations - About 7 hrs to fix
examples/hierarchical_strategy_for_one-component/generate_microscopic-c.py on lines 20..28
examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py on lines 19..27

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 121.

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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