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

for pidCG in range(int(num_particlesCG)):
    # we put CG molecule in first atom, later CG molecules will be positioned in the center
    #cmp = espressopp.tools.AdressSetCG(3, pidCG, allParticlesAT)

    # Preparation of tuples (tuples define, which atoms belong to which CG molecules)
Severity: Major
Found in examples/adress/hadress_water/water.py and 1 other location - About 3 days to fix
examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py on lines 117..147

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 333.

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 add_particles_array:

        tstart = time.time()
        props = ['id', 'type', 'mass', 'posx', 'posy', 'posz', 'vx', 'vy', 'vz']
        ids      = np.arange(1,num_particles+1)
Severity: Major
Found in examples/add_particles_numpy/add_particles_numpy.py and 1 other location - About 2 days to fix
testsuite/storage/testAddParticlesArray.py on lines 60..85

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 302.

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 add_particles_array:

        tstart = time.time()
        props = ['id', 'type', 'mass', 'posx', 'posy', 'posz', 'vx', 'vy', 'vz']
        ids      = np.arange(1,num_particles+1)
Severity: Major
Found in testsuite/storage/testAddParticlesArray.py and 1 other location - About 2 days to fix
examples/add_particles_numpy/add_particles_numpy.py on lines 39..64

Duplicated Code

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

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

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

Tuning

This issue has a mass of 302.

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(1,P):
        for p in allParticles:
            pid=p[propDict['id']]
            newparticle=copy.deepcopy(p)
            # set types accoring to imag time index
Severity: Major
Found in src/tools/pathintegral.py and 1 other location - About 2 days to fix
testsuite/pi_water/pathintegral.py on lines 69..82

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 285.

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(1,P):
        for p in allParticles:
            pid=p[propDict['id']]
            newparticle=copy.deepcopy(p)
            # set new types
Severity: Major
Found in testsuite/pi_water/pathintegral.py and 1 other location - About 2 days to fix
src/tools/pathintegral.py on lines 110..123

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 285.

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(nInteractions):
        bT = system.getInteraction(i).bondType()
        if   bT == espressopp.interaction.Pair:
            nbondtypes += 1
            bl  = system.getInteraction(i).getFixedPairList().getBonds()
Severity: Major
Found in src/tools/io_extended.py and 1 other location - About 2 days to fix
src/tools/lammps.py on lines 405..427

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 276.

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(nInteractions):
        bT = system.getInteraction(i).bondType()
        if   bT == espressopp.interaction.Pair:
            nbondtypes += 1
            bl  = system.getInteraction(i).getFixedPairList().getBonds()
Severity: Major
Found in src/tools/lammps.py and 1 other location - About 2 days to fix
src/tools/io_extended.py on lines 74..96

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 276.

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

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

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

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

Refactorings

Further Reading

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

for pidCG in range(num_particlesCG):
    # we put CG molecule in first atom, later CG molecules will be positioned in the center
    cmp = espressopp.tools.AdressSetCG(4, pidCG, allParticlesAT)
    # Preparation of tuples (tuples define, which atoms belong to which CG molecules)
    tmptuple = [pidCG+num_particles]
Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py and 2 other locations - About 2 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py on lines 100..126
examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py on lines 96..122

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 258.

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

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

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

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

Refactorings

Further Reading

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

for pidCG in range(num_particlesCG):
    # we put CG molecule in first atom, later CG molecules will be positioned in the center
    cmp = espressopp.tools.AdressSetCG(4, pidCG, allParticlesAT)
    # Preparation of tuples (tuples define, which atoms belong to which CG molecules)
    tmptuple = [pidCG+num_particles]
Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py and 2 other locations - About 2 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py on lines 96..122
examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py on lines 96..122

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 258.

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

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

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

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

Refactorings

Further Reading

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

for pidCG in range(num_particlesCG):
    # we put CG molecule in first atom, later CG molecules will be positioned in the center
    cmp = espressopp.tools.AdressSetCG(4, pidCG, allParticlesAT)
    # Preparation of tuples (tuples define, which atoms belong to which CG molecules)
    tmptuple = [pidCG+num_particles]
Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py and 2 other locations - About 2 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py on lines 100..126
examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py on lines 96..122

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 258.

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

        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), espressopp.Real3D(0.0, 1.0, 0.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(5.0, 6.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
            (3, 1, 0, espressopp.Real3D(5.0, 7.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
            (4, 1, 0, espressopp.Real3D(5.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 2 other locations - About 2 days to fix
testsuite/AdResS/TDforce/test_TDforce.py on lines 204..214
testsuite/AdResS/TDforce/test_TDforce.py on lines 257..267

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 256.

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

        particle_list = [
            (1, 1, 0, espressopp.Real3D(4.0, 5.0, 5.0), espressopp.Real3D(-1.0, 1.0, 0.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), espressopp.Real3D(1.0, 1.0, 0.0), 1.0, 0),
            (3, 1, 0, espressopp.Real3D(5.0, 6.2, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
            (4, 1, 0, espressopp.Real3D(3.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 2 other locations - About 2 days to fix
testsuite/AdResS/TDforce/test_TDforce.py on lines 151..161
testsuite/AdResS/TDforce/test_TDforce.py on lines 204..214

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 256.

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

        particle_list = [
            (1, 1, 0, espressopp.Real3D(4.0, 5.0, 5.0), espressopp.Real3D(-1.0, 1.0, 0.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), espressopp.Real3D(1.0, 1.0, 0.0), 1.0, 0),
            (3, 1, 0, espressopp.Real3D(5.0, 6.2, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
            (4, 1, 0, espressopp.Real3D(3.0, 8.5, 5.0), espressopp.Real3D(0.0, 0.0, 0.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 2 other locations - About 2 days to fix
testsuite/AdResS/TDforce/test_TDforce.py on lines 151..161
testsuite/AdResS/TDforce/test_TDforce.py on lines 257..267

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 256.

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

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

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

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

Refactorings

Further Reading

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

class VerletListLennardJonesLocal(InteractionLocal, vec_interaction_VerletListLennardJones):

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 250.

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

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

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

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

Refactorings

Further Reading

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

class VerletListLennardJonesBaseLocal(InteractionLocal, vec_interaction_VerletListLennardJonesBase):

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 250.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 238.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 238.

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

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

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

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

Refactorings

Further Reading

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

    def test_simple_gromacs(self):
        particle_list = [
            (1, espressopp.Real3D(2.2319834598, 3.5858734534, 4.7485623451), espressopp.Real3D(2.2319834598, 1.5556734534, 4.7485623451), 0),
            (2, espressopp.Real3D(6.3459834598, 9.5858734534, 16.7485623451), espressopp.Real3D(3.2319834598, 1.5858734534, 1.7485623451), 0),
            (3, espressopp.Real3D(2.2319834598, 15.5858734534, 5.7485623451), espressopp.Real3D(4.2319834598, 2.5858734534, 2.7485623451), 2),
Severity: Major
Found in testsuite/FileIOTests/dump_gromacs/test_dump_gromacs.py and 1 other location - About 1 day to fix
testsuite/FileIOTests/dump_xyz/test_dump_xyz.py on lines 87..100

Duplicated Code

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

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

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

Tuning

This issue has a mass of 212.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 212.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 200.

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

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

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

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

Refactorings

Further Reading

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