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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 151.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 151.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 150.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 150.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 146.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 146.

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

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

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

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

Refactorings

Further Reading

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

            for j in range (halo, myNi[1]-halo):
                for k in range (halo, myNi[2]-halo):
                    av_den += self.lb.getLBMom(Int3D(i,j,k), 0)

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 141.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 141.

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

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

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

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

Refactorings

Further Reading

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

    if(num_bonds != 0):
        # find and store bond coeff
        line = ''
        while not 'Bond Coeffs' in line:
            line = f.readline()
Severity: Major
Found in src/tools/lammps.py and 1 other location - About 1 day to fix
src/tools/lammps.py on lines 290..304

Duplicated Code

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

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

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

Tuning

This issue has a mass of 141.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 141.

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

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

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

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

Refactorings

Further Reading

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 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

Identical blocks of code found in 7 locations. Consider refactoring.
Open

    def setUp(self):

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

Identical blocks of code found in 7 locations. Consider refactoring.
Open

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 138.

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

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

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

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

Refactorings

Further Reading

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