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Function read has a Cognitive Complexity of 117 (exceeds 5 allowed). Consider refactoring.
Open

def read(file):
    """ Read ESPResSo data files.

    Keyword argument:
    file -- contains simulation variables, data of all particles, and information about bonds.
Severity: Minor
Found in src/tools/espresso_old.py - About 2 days 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

class VerletListLennardJonesLocal(InteractionLocal, vec_interaction_VerletListLennardJones):

    def __init__(self, vl):
        if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
            cxxinit(self, vec_interaction_VerletListLennardJones, vl)
Severity: Major
Found in src/vec/interaction/LennardJones.py and 1 other location - About 2 days to fix
src/vec/interaction/LennardJones.py on lines 43..59

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 250.

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

class VerletListLennardJonesBaseLocal(InteractionLocal, vec_interaction_VerletListLennardJonesBase):

    def __init__(self, vl):
        if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
            cxxinit(self, vec_interaction_VerletListLennardJonesBase, vl)
Severity: Major
Found in src/vec/interaction/LennardJones.py and 1 other location - About 2 days to fix
src/vec/interaction/LennardJones.py on lines 61..77

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 250.

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 n > round((2. * eh_size) / (rc + skin) - 0.5 + 2.) and min(boxList) / (rc + skin) < 4.:
                            boxList = [slabMSDims[0] * ((2. * eh_size) + 2. * (rc + skin)), slabMSDims[1] * ((2. * eh_size) + 2. * (rc + skin)), slabMSDims[2] * ((2. * eh_size) + 2. * (rc + skin))]
                            boxList = [(1 - slabMSDims[0]) * box_size[0] + boxList[0], (1 - slabMSDims[1]) * box_size[1] + boxList[1], (1 - slabMSDims[2]) * box_size[2] + boxList[2]]
                            # boxList=[box_size[0],box_size[1],box_size[2]]     # UJ is here
                            print("HeSpaDDA message: this option THREE of the ideal gas size box your low resolution region is just sufficiently big")
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 2 days to fix
src/tools/decomp.py on lines 151..154

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 238.

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 n <= round((2. * eh_size) / (rc + skin) - 0.5 + 2.) and min(boxList) * ratioEHCG / (rc + skin) >= 1.:
                            boxList = [slabMSDims[0] * ((2. * eh_size) + 2. * (rc + skin)), slabMSDims[1] * ((2. * eh_size) + 2. * (rc + skin)), slabMSDims[2] * ((2. * eh_size) + 2. * (rc + skin))]
                            boxList = [(1 - slabMSDims[0]) * box_size[0] + boxList[0], (1 - slabMSDims[1])* box_size[1] + boxList[1], (1 - slabMSDims[2]) * box_size[2] + boxList[2]]
                            print("HeSpaDDA message: this option ONE of the ideal gas size box your low resolution region is small")
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 2 days to fix
src/tools/decomp.py on lines 160..164

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 238.

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

File LennardJones.py has 844 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#  Copyright (C) 2012-2018
#      Max Planck Institute for Polymer Research
#  Copyright (C) 2008-2011
#      Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
Severity: Major
Found in src/interaction/LennardJones.py - About 2 days to fix

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

        def test_simple_gromacs(self):
        particle_list = [
            (1, espressopp.Real3D(2.2319834598, 3.5858734534, 4.7485623451), espressopp.Real3D(2.2319834598, 1.5556734534, 4.7485623451), 0),
            (2, espressopp.Real3D(6.3459834598, 9.5858734534, 16.7485623451), espressopp.Real3D(3.2319834598, 1.5858734534, 1.7485623451), 0),
            (3, espressopp.Real3D(2.2319834598, 15.5858734534, 5.7485623451), espressopp.Real3D(4.2319834598, 2.5858734534, 2.7485623451), 2),
    Severity: Major
    Found in testsuite/FileIOTests/dump_gromacs/test_dump_gromacs.py and 1 other location - About 1 day to fix
    testsuite/FileIOTests/dump_xyz/test_dump_xyz.py on lines 87..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 212.

    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 test_standard_xyz(self):
        particle_list = [
            (1, espressopp.Real3D(2.2319834598, 3.5858734534, 4.7485623451), espressopp.Real3D(2.2319834598, 1.5556734534, 4.7485623451), 0),
            (2, espressopp.Real3D(6.3459834598, 9.5858734534, 16.7485623451), espressopp.Real3D(3.2319834598, 1.5858734534, 1.7485623451), 0),
            (3, espressopp.Real3D(2.2319834598, 15.5858734534, 5.7485623451), espressopp.Real3D(4.2319834598, 2.5858734534, 2.7485623451), 2),
    Severity: Major
    Found in testsuite/FileIOTests/dump_xyz/test_dump_xyz.py and 1 other location - About 1 day to fix
    testsuite/FileIOTests/dump_gromacs/test_dump_gromacs.py on lines 76..88

    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 212.

    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 src/bc/OrthorhombicBC.py and 1 other location - About 1 day to fix
    src/bc/SlabBC.py on lines 0..75

    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 200.

    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 src/bc/SlabBC.py and 1 other location - About 1 day to fix
    src/bc/OrthorhombicBC.py on lines 0..73

    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 200.

    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 createPathintegralSystem has a Cognitive Complexity of 88 (exceeds 5 allowed). Consider refactoring.
    Open

    def createPathintegralSystem(allParticles,
props,
types,
system,
exclusions,
    Severity: Minor
    Found in src/tools/pathintegral.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

    def readingDesernoForcesFile():
    # forces x,y,z
    fx, fy, fz = [], [], []
    # energy
    energy = 0.0
    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 39..64

    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 190.

    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 readingDesernoForcesFile():
    # forces x,y,z
    fx, fy, fz = [], [], []
    # energy
    energy = 0.0
    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 40..65

    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 190.

    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

        for i in range(num_molecule_copies):
        for j in range(dihedrals_per_mol):
            pid1, pid2, pid3, pid4, dihtypeid = dihedrals_tmp[j][0:5]
            ia=molstartindex+pid1 + (i * num_atoms_molecule) # index of copy atom i
            ib=molstartindex+pid2 + (i * num_atoms_molecule) # index of copy atom j
    Severity: Major
    Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
    src/tools/gromacs.py on lines 939..949

    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 188.

    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

        for i in range(num_molecule_copies):
        for j in range(impropers_per_mol):
            pid1, pid2, pid3, pid4, dihtypeid = impropers_tmp[j][0:5]
            ia=molstartindex+pid1 + (i * num_atoms_molecule) # index of copy atom i
            ib=molstartindex+pid2 + (i * num_atoms_molecule) # index of copy atom j
    Severity: Major
    Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
    src/tools/gromacs.py on lines 857..867

    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 188.

    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

    File Tabulated.py has 669 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    #  Copyright (C) 2017,2018
#      Max Planck Institute for Polymer Research
#  Copyright (C) 2016
#      Jakub Krajniak (jkrajniak at gmail.com)
#  Copyright (C) 2012,2013,2014,2015
    Severity: Major
    Found in src/interaction/Tabulated.py - About 1 day to fix

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

      for part in range(num_atoms//3):
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
    bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))
      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 147..150

      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 169.

      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 part in range(num_atoms/3):
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
            bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))
      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 197..200

      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 169.

      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/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py and 1 other location - About 1 day to fix
      examples/hierarchical_strategy_for_one-component/reinsertion.py on lines 65..78

      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 163.

      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/hierarchical_strategy_for_one-component/reinsertion.py and 1 other location - About 1 day to fix
      examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py on lines 50..63

      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 163.

      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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