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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 200.

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

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

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

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

Refactorings

Further Reading

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

def readingDesernoForcesFile():
    # forces x,y,z
    fx, fy, fz = [], [], []
    # energy
    energy = 0.0
Severity: Major
Found in examples/ewald/ewald.py and 1 other location - About 1 day to fix
testsuite/ewald/ewald_eppDeserno_comparison.py on lines 39..64

Duplicated Code

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

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

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

Tuning

This issue has a mass of 190.

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

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

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

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

Refactorings

Further Reading

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

def readingDesernoForcesFile():
    # forces x,y,z
    fx, fy, fz = [], [], []
    # energy
    energy = 0.0
Severity: Major
Found in testsuite/ewald/ewald_eppDeserno_comparison.py and 1 other location - About 1 day to fix
examples/ewald/ewald.py on lines 40..65

Duplicated Code

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

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

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

Tuning

This issue has a mass of 190.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 188.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 188.

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

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

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

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

Refactorings

Further Reading

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

for part in range(num_atoms//3):
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
    bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
    bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))
Severity: Major
Found in examples/adress/piadress_water/AdaptivePIwater.py and 1 other location - About 1 day to fix
testsuite/AdResS/PIAdResS/test_PIAdResS.py on lines 147..150

Duplicated Code

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

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

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

Tuning

This issue has a mass of 169.

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

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

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

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

Refactorings

Further Reading

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

        for part in range(num_atoms/3):
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+1))
            bondsOH.append((num_Trotter_beads + 1 + 3*part, num_Trotter_beads + 1 + 3*part+2))
            bondsHH.append((num_Trotter_beads + 1 + 3*part+1, num_Trotter_beads + 1 + 3*part+2))
Severity: Major
Found in testsuite/AdResS/PIAdResS/test_PIAdResS.py and 1 other location - About 1 day to fix
examples/adress/piadress_water/AdaptivePIwater.py on lines 197..200

Duplicated Code

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

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

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

Tuning

This issue has a mass of 169.

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

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

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

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

Refactorings

Further Reading

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

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py and 1 other location - About 1 day to fix
examples/hierarchical_strategy_for_one-component/reinsertion.py on lines 65..78

Duplicated Code

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

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

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

Tuning

This issue has a mass of 163.

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

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

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

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

Refactorings

Further Reading

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

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/hierarchical_strategy_for_one-component/reinsertion.py and 1 other location - About 1 day to fix
examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py on lines 50..63

Duplicated Code

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

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

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

Tuning

This issue has a mass of 163.

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

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

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

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

Refactorings

Further Reading

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

        for i in range(2, 6):
            particle = self.system.storage.getParticle(i)
            mass.append(particle.mass)
            diff = []
            for j in range(3):
Severity: Major
Found in testsuite/constrain_com/testCaseConstrainCOM.py and 1 other location - About 1 day to fix
testsuite/constrain_com/testCaseConstrainCOM.py on lines 138..146

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 162.

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)
            mass.append(particle.mass)
            diff = []
            for j in range(3):
Severity: Major
Found in testsuite/constrain_com/testCaseConstrainCOM.py and 1 other location - About 1 day to fix
testsuite/constrain_com/testCaseConstrainCOM.py on lines 106..114

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 162.

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

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

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

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

Refactorings

Further Reading

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

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/adress/fadress_tetraliquid/adress.py and 1 other location - About 1 day to fix
examples/convert_gromacs_tables/convert_gromacs_table.py on lines 71..84

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 161.

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

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

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

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

Refactorings

Further Reading

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

def writeTabFile(pot, name, N, low=0.0, high=2.5, body=2):
    outfile = open(name, "w")
    delta = (high - low) / (N - 1)

    for i in range(int(N)):
Severity: Major
Found in examples/convert_gromacs_tables/convert_gromacs_table.py and 1 other location - About 1 day to fix
examples/adress/fadress_tetraliquid/adress.py on lines 52..66

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 161.

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, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
            (2, 1, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
            (3, 1, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 0),
            (4, 1, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 45..55
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 186..196

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 156.

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, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
            (2, 1, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
            (3, 1, espressopp.Real3D(5.0, 7.5, 5.0), 1.0, 0),
            (4, 1, espressopp.Real3D(5.0, 8.5, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 45..55
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 116..126

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 156.

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, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
            (2,  1, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
            (3,  1, espressopp.Real3D(7.5, 5.0, 5.0), 1.0, 0),
            (4,  1, espressopp.Real3D(8.5, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 2 other locations - About 1 day to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 116..126
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 186..196

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 156.

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(0, num_particles):
    print((format2 % (j, ' ', \
                         system.storage.getParticle(j).f.x, ' ', \
                         system.storage.getParticle(j).f.y, ' ', \
                         system.storage.getParticle(j).f.z, \
Severity: Major
Found in examples/ewald/ewald.py and 1 other location - About 1 day to fix
testsuite/ewald/ewald_eppDeserno_comparison.py on lines 176..184

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 154.

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(0, num_particles):
    print((format2 % (j, ' ', \
                         system.storage.getParticle(j).f.x, ' ', \
                         system.storage.getParticle(j).f.y, ' ', \
                         system.storage.getParticle(j).f.z, \
Severity: Major
Found in testsuite/ewald/ewald_eppDeserno_comparison.py and 1 other location - About 1 day to fix
examples/ewald/ewald.py on lines 177..185

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 154.

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 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

    if defaults:
        if int(defaults['combinationrule'])==1:
            for atnr, at in atomtypeparams.items():
                c6=float(at['sig'])
                c12=float(at['eps'])
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 1 day to fix
src/tools/gromacs.py on lines 1190..1199

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

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