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src/tools/decomp.py

Summary

Maintainability
F
1 mo
Test Coverage

Function nodeGrid has a Cognitive Complexity of 225 (exceeds 5 allowed). Consider refactoring.
Open

def nodeGrid(n=None, box_size=None, rc=None, skin=None, eh_size=0, ratioMS=0, idealGas=0, slabMSDims=[0, 0, 0,]):
    if isinstance(n, numbers.Number) and box_size is None:
        return nodeGridSimple(n)
    else:
        if eh_size!=0:
Severity: Minor
Found in src/tools/decomp.py - About 4 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

File decomp.py has 463 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#  Copyright (C) 2020(H)
#      Jozef Stefan Institute
#      Max Planck Institute for Polymer Research
#  Copyright (C) 2012,2013,2017,2018(H)
#      Max Planck Institute for Polymer Research
Severity: Minor
Found in src/tools/decomp.py - About 7 hrs to fix

    Function cherrypickTotalProcs has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
    Open

    def cherrypickTotalProcs(box_size, rc, skin, MnN, CpN, percTol=0.2, eh_size=0, ratioMS=0, idealGas=0, slabMSDims=[0, 0, 0]):
    indMax = max(box_size)
    indMin = min(box_size)
    L_l = box_size[indMax]
    L_s = box_size[indMin]
    Severity: Minor
    Found in src/tools/decomp.py - About 3 hrs 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

    Function neiListAdress has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
    Open

    def neiListAdress(node_grid, box_size, rc, skin, eh_size, adrCenter, ratioMS, idealGasFlag=True, sphereAdr=False, slabMSDims=[1, 0, 0], halfCellInt=1):
    # dataStructure Initialization
    print("HeSpaDDA message: Current heterogeneous NodeGrid (X,Y,Z)", node_grid)
    rc_skin = rc + skin
    # define Neighbor vectors
    Severity: Minor
    Found in src/tools/decomp.py - About 3 hrs 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

    Consider simplifying this complex logical expression.
    Open

            if (indMax == 0 and indMin == 1) or (indMax == 0 and indMin == 2):
            if nX[i] > (SymFactor - percTol * SymFactor) * nY[i] and nX[i] < (SymFactor + percTol * SymFactor) * nY[i]:
                pickedP.append(i)
        elif (indMax == 1 and indMin == 0) or (indMax == 1 and indMin == 2):
            if nY[i] > (SymFactor - percTol * SymFactor) * nX[i] and nY[i] < (SymFactor + percTol * SymFactor) * nX[i]:
    Severity: Critical
    Found in src/tools/decomp.py - About 2 hrs to fix

      Function neiListAdress has 11 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def neiListAdress(node_grid, box_size, rc, skin, eh_size, adrCenter, ratioMS, idealGasFlag=True, sphereAdr=False, slabMSDims=[1, 0, 0], halfCellInt=1):
      Severity: Major
      Found in src/tools/decomp.py - About 1 hr to fix

        Function nodeGridSimple has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
        Open

        def nodeGridSimple(n):  # Mainly used for Lattice-Boltzmann and cubic geometries
    ijkmax = 3 * n * n + 1
    d1 = 1
    d2 = 1
    d3 = 1
        Severity: Minor
        Found in src/tools/decomp.py - About 1 hr 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

        Function cherrypickTotalProcs has 10 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def cherrypickTotalProcs(box_size, rc, skin, MnN, CpN, percTol=0.2, eh_size=0, ratioMS=0, idealGas=0, slabMSDims=[0, 0, 0]):
        Severity: Major
        Found in src/tools/decomp.py - About 1 hr to fix

          Function nodeGrid has 8 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def nodeGrid(n=None, box_size=None, rc=None, skin=None, eh_size=0, ratioMS=0, idealGas=0, slabMSDims=[0, 0, 0,]):
          Severity: Major
          Found in src/tools/decomp.py - About 1 hr to fix

            Function tuneSkin has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
            Open

            def tuneSkin(system, integrator, minSkin=0.01, maxSkin=1.5, precision=0.001, printInfo=True):
    if printInfo:
        print('HeSpaDDA message: The tuning is started. It can take some time depending on your system.')

    fi = (1.0 + math.sqrt(5.0)) / 2.0  # golden ratio
            Severity: Minor
            Found in src/tools/decomp.py - About 55 mins 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

            Avoid deeply nested control flow statements.
            Open

                                for j in range(i, n + 1):
                        for k in range(j, n + 1):
                            if (i * j * k == n) and (i * i + j * j + k * k < ijkmax):
                                dN[0] = k
                                dN[1] = j
            Severity: Major
            Found in src/tools/decomp.py - About 45 mins to fix

              Avoid deeply nested control flow statements.
              Open

                                  if sum(slabMSDims) > 0.1:
                        boxList = [slabMSDims[0] * (box_size[0] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.)), slabMSDims[1] * (box_size[1] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.)), slabMSDims[2] * (box_size[2] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.))]
                        boxList = [(1 - slabMSDims[0]) * box_size[0] * (pow(ratioMS, 0.3333)) + boxList[0], (1 - slabMSDims[1]) * box_size[1] * (pow(ratioMS, 0.3333)) + boxList[1], (1 - slabMSDims[2]) * box_size[2] * (pow(ratioMS, 0.3333)) + boxList[2]]  # Flag NOR

                    else:
              Severity: Major
              Found in src/tools/decomp.py - About 45 mins to fix

                Avoid deeply nested control flow statements.
                Open

                                    for j in range(i, n + 1):
                        if (i * i * j == n) and (i * i + j * j + i * i < ijkmax):
                            dN[0] = j
                            dN[1] = i
                            dN[2] = i
                Severity: Major
                Found in src/tools/decomp.py - About 45 mins to fix

                  Avoid deeply nested control flow statements.
                  Open

                                      if sum(slabMSDims) > 0:
                        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 - About 45 mins to fix

                    Function tuneSkin has 6 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                    def tuneSkin(system, integrator, minSkin=0.01, maxSkin=1.5, precision=0.001, printInfo=True):
                    Severity: Minor
                    Found in src/tools/decomp.py - About 45 mins to fix

                      Avoid deeply nested control flow statements.
                      Open

                                          for j in range(i, n + 1):
                        if (i * i * j == n) and (i * i + j * j + i * i < ijkmax):
                            dN[0] = j
                            dN[1] = i
                            dN[2] = i
                      Severity: Major
                      Found in src/tools/decomp.py - About 45 mins to fix

                        Avoid deeply nested control flow statements.
                        Open

                                            for j in range(i, n + 1):
                        for k in range(j, n + 1):
                            if (i * j * k == n) and (i * i + j * j + k * k < ijkmax):
                                dN[0] = k
                                dN[1] = j
                        Severity: Major
                        Found in src/tools/decomp.py - About 45 mins to fix

                          Function neiListHom has 5 arguments (exceeds 4 allowed). Consider refactoring.
                          Open

                          def neiListHom(node_grid, box, rc, skin, halfCellInt = 1):
                          Severity: Minor
                          Found in src/tools/decomp.py - About 35 mins to fix

                            Function printTimeVsSkin has 5 arguments (exceeds 4 allowed). Consider refactoring.
                            Open

                            def printTimeVsSkin(system, integrator, minSkin=0.01, maxSkin=1.5, skinStep=0.005):
                            Severity: Minor
                            Found in src/tools/decomp.py - About 35 mins to fix

                              Function cellGrid has 5 arguments (exceeds 4 allowed). Consider refactoring.
                              Open

                              def cellGrid(box_size, node_grid, rc, skin, halfCellInt = 1):
                              Severity: Minor
                              Found in src/tools/decomp.py - About 35 mins to fix

                                Function cellGrid has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                                Open

                                def cellGrid(box_size, node_grid, rc, skin, halfCellInt = 1):
    rc_skin = rc + skin
    if rc_skin == 0:
        raise Error("interaction range (cutoff + skin) must be larger than 0")
    if (node_grid[0] <= 0 or node_grid[1] <= 0 or node_grid[2] <= 0):
                                Severity: Minor
                                Found in src/tools/decomp.py - About 25 mins 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 ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[2]) < (1* (rc + skin)))) and not ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) and (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin)))):
                print('HeSpaDDA message: Non AdResS DD with 2 equal dimensions!')
                for i in range(1, n + 1):
                    for j in range(i, n + 1):
                        if (i * i * j == n) and (i * i + j * j + i * i < ijkmax):
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 2 wks to fix
                                src/tools/decomp.py on lines 179..232

                                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 1375.

                                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 ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[2]) < (1* (rc + skin)))) and not ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) and (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin)))):
                print('HeSpaDDA message: AdResS DD with 2 equal dimensions!')
                for i in range(1, n + 1):
                    for j in range(i, n + 1):
                        if (i * i * j == n) and (i * i + j * j + i * i < ijkmax):
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 2 wks to fix
                                src/tools/decomp.py on lines 254..309

                                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 1375.

                                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

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

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

                                Duplicated Code

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

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

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

                                Tuning

                                This issue has a mass of 150.

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

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

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

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

                                Refactorings

                                Further Reading

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

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

                                Duplicated Code

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

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

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

                                Tuning

                                This issue has a mass of 150.

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

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

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

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

                                Refactorings

                                Further Reading

                                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

                                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

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

                                            if abs(box_size[1] - box_size[2]) < (2 * (rc + skin)):
                if fdN[2] > fdN[1]:
                    aux = fdN[2]
                    fdN[2] = fdN[1]
                    fdN[1] = aux
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 7 hrs to fix
                                src/tools/decomp.py on lines 310..318

                                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 113.

                                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 abs(box_size[1] - box_size[2]) < (2 * (rc + skin)):
        if fdN[2] > fdN[1]:
            aux = fdN[2]
            fdN[2] = fdN[1]
            fdN[1] = aux
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 7 hrs to fix
                                src/tools/decomp.py on lines 233..241

                                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 113.

                                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 (indMax == 0 and indMin == 1) or (indMax == 0 and indMin == 2):
            if nX[i] > (SymFactor - percTol * SymFactor) * nY[i] and nX[i] < (SymFactor + percTol * SymFactor) * nY[i]:
                pickedP.append(i)
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 5 hrs to fix
                                src/tools/decomp.py on lines 384..386
                                src/tools/decomp.py on lines 387..389

                                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 90.

                                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

                                        elif (indMax == 1 and indMin == 0) or (indMax == 1 and indMin == 2):
            if nY[i] > (SymFactor - percTol * SymFactor) * nX[i] and nY[i] < (SymFactor + percTol * SymFactor) * nX[i]:
                pickedP.append(i)
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 5 hrs to fix
                                src/tools/decomp.py on lines 381..383
                                src/tools/decomp.py on lines 387..389

                                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 90.

                                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

                                        elif (indMax == 2 and indMin == 0) or (indMax == 2 and indMin == 1):
            if nZ[i] > (SymFactor - percTol * SymFactor) * nX[i] and nZ[i] < (SymFactor + percTol * SymFactor) * nX[i]:
                pickedP.append(i)
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 5 hrs to fix
                                src/tools/decomp.py on lines 381..383
                                src/tools/decomp.py on lines 384..386

                                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 90.

                                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

                                                        boxList = [slabMSDims[0] * (box_size[0] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.)), slabMSDims[1] * (box_size[1] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.)), slabMSDims[2] * (box_size[2] + (2. * eh_size) * (pow(ratioMS, 0.3333) - 1.))]
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 1 hr to fix
                                src/tools/decomp.py on lines 138..138
                                src/tools/decomp.py on lines 138..138

                                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 48.

                                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 (node_grid[0] <= 0 or node_grid[1] <= 0 or node_grid[2] <= 0):
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 1 hr to fix
                                src/standard_system/LennardJones.py on lines 75..75
                                src/standard_system/PolymerMelt.py on lines 77..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 43.

                                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

                                        nX[i - 1], nY[i - 1], nZ[i - 1] = nodeGrid(procArray[i - 1], box_size, rc, skin, eh_size, ratioMS, idealGas, slabMSDims)
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 1 hr to fix
                                testsuite/HeSpaDDA/nodeGrids/testHeSpaDDAv1p1.py on lines 65..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 42.

                                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

                                                        elif n > round((2. * eh_size) / (rc + skin) - 0.5 + 2.) and min(boxList) / (rc + skin) >= 4. and round((2. * eh_size) / (rc + skin) - 0.5 + 2.) > min(boxList) / (rc + skin):
                                Severity: Major
                                Found in src/tools/decomp.py and 1 other location - About 1 hr to fix
                                src/tools/decomp.py on lines 160..160

                                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 41.

                                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

                                    ix = (box_size[0] * halfCellInt) / (rc_skin * node_grid[0])
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 45 mins to fix
                                src/tools/decomp.py on lines 333..333
                                src/tools/decomp.py on lines 337..337

                                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 35.

                                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

                                    iy = (box_size[1] * halfCellInt) / (rc_skin * node_grid[1])
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 45 mins to fix
                                src/tools/decomp.py on lines 328..328
                                src/tools/decomp.py on lines 337..337

                                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 35.

                                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

                                    iz = (box_size[2] * halfCellInt) / (rc_skin * node_grid[2])
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 45 mins to fix
                                src/tools/decomp.py on lines 328..328
                                src/tools/decomp.py on lines 333..333

                                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 35.

                                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

                                            ratioEH2CG = [(2. * eh_size) / (abs(box_size[0] - (2. * eh_size))), (2. * eh_size)/(abs(box_size[1] - (2. * eh_size))), (2. * eh_size) / (abs(box_size[2] - (2. * eh_size)))]
                                Severity: Major
                                Found in src/tools/decomp.py and 2 other locations - About 45 mins to fix
                                src/tools/decomp.py on lines 130..130
                                src/tools/decomp.py on lines 130..130

                                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 35.

                                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

                                    cellsY = halfCellInt * round(cursor[1] / rc_skin - 0.5)
                                Severity: Minor
                                Found in src/tools/decomp.py and 2 other locations - About 35 mins to fix
                                src/tools/decomp.py on lines 434..434
                                src/tools/decomp.py on lines 436..436

                                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 33.

                                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

                                    cellsX = halfCellInt * round(cursor[0] / rc_skin - 0.5)
                                Severity: Minor
                                Found in src/tools/decomp.py and 2 other locations - About 35 mins to fix
                                src/tools/decomp.py on lines 435..435
                                src/tools/decomp.py on lines 436..436

                                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 33.

                                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

                                    cellsZ = halfCellInt * round(cursor[2] / rc_skin - 0.5)
                                Severity: Minor
                                Found in src/tools/decomp.py and 2 other locations - About 35 mins to fix
                                src/tools/decomp.py on lines 434..434
                                src/tools/decomp.py on lines 435..435

                                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 33.

                                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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