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

            if ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin))) or (abs(box_size[0] - box_size[2]) < (1* (rc + skin)))) and not ((abs(box_size[1] - box_size[2]) < (1.0* (rc + skin))) and (abs(box_size[0] - box_size[1]) < (1.0* (rc + skin)))):
                print('HeSpaDDA message: Non AdResS DD with 2 equal dimensions!')
                for i in range(1, n + 1):
                    for j in range(i, n + 1):
                        if (i * i * j == n) and (i * i + j * j + i * i < ijkmax):
Severity: Major
Found in src/tools/decomp.py and 1 other location - About 2 wks to fix
src/tools/decomp.py on lines 179..232

Duplicated Code

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

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

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

Tuning

This issue has a mass of 1375.

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

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

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

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

Refactorings

Further Reading

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

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

Duplicated Code

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

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

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

Tuning

This issue has a mass of 1375.

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

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

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

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

Refactorings

Further Reading

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

    def test_ATATCG_template(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/HAdResS/test_HAdResS.py and 1 other location - About 1 wk to fix
testsuite/AdResS/ForceAdResS/test_AdResS.py on lines 254..324

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 979.

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_ATATCG_template(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/ForceAdResS/test_AdResS.py and 1 other location - About 1 wk to fix
testsuite/AdResS/HAdResS/test_HAdResS.py on lines 184..254

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 979.

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_ATAT_CG_templates_HAdResS(self):
        # add atomistic interactions
        interNBat = espressopp.interaction.VerletListHadressATLenJonesReacFieldGen(self.vl, self.ftpl)
        potLJ  = espressopp.interaction.LennardJones(epsilon=0.650299305951, sigma=0.316549165245, shift='auto', cutoff=1.4)
        potQQ  = espressopp.interaction.ReactionFieldGeneralized(prefactor=138.935485, kappa=0.0, epsilon1=1.0, epsilon2=80.0, cutoff= 1.4, shift="auto")
Severity: Major
Found in testsuite/AdResS/MTSAdResS/test_MTSAdResS.py and 1 other location - About 6 days to fix
testsuite/AdResS/MTSAdResS/test_MTSAdResS.py on lines 166..212

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 693.

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_ATAT_CG_templates_FAdResS(self):
        # add atomistic interactions
        interNBat = espressopp.interaction.VerletListAdressATLenJonesReacFieldGen(self.vl, self.ftpl)
        potLJ  = espressopp.interaction.LennardJones(epsilon=0.650299305951, sigma=0.316549165245, shift='auto', cutoff=1.4)
        potQQ  = espressopp.interaction.ReactionFieldGeneralized(prefactor=138.935485, kappa=0.0, epsilon1=1.0, epsilon2=80.0, cutoff= 1.4, shift="auto")
Severity: Major
Found in testsuite/AdResS/MTSAdResS/test_MTSAdResS.py and 1 other location - About 6 days to fix
testsuite/AdResS/MTSAdResS/test_MTSAdResS.py on lines 72..118

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 693.

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

Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/Tetracryst.py and 2 other locations - About 6 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/Tetracryst.py on lines 0..88
examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/Tetracryst.py on lines 0..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 686.

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

Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/Tetracryst.py and 2 other locations - About 6 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/Tetracryst.py on lines 0..88
examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/Tetracryst.py on lines 0..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 686.

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

Severity: Major
Found in examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/Tetracryst.py and 2 other locations - About 6 days to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/Tetracryst.py on lines 0..88
examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/Tetracryst.py on lines 0..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 686.

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_AT_CG_templates_FAdResS(self):
        # add atomistic interaction
        interNBat = espressopp.interaction.VerletListAdressATLennardJones(self.vl, self.ftpl)
        potLJ  = espressopp.interaction.LennardJones(epsilon=0.650299305951, sigma=0.316549165245, shift='auto', cutoff=1.4)
        interNBat.setPotential(type1=0, type2=0, potential=potLJ)
Severity: Major
Found in testsuite/AdResS/MTSAdResS/test_MTSAdResS.py and 1 other location - About 6 days to fix
testsuite/AdResS/MTSAdResS/test_MTSAdResS.py on lines 120..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 646.

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_AT_CG_templates_HAdResS(self):
        # add atomistic interaction
        interNBat = espressopp.interaction.VerletListHadressATLennardJones(self.vl, self.ftpl)
        potLJ  = espressopp.interaction.LennardJones(epsilon=0.650299305951, sigma=0.316549165245, shift='auto', cutoff=1.4)
        interNBat.setPotential(type1=0, type2=0, potential=potLJ)
Severity: Major
Found in testsuite/AdResS/MTSAdResS/test_MTSAdResS.py and 1 other location - About 6 days to fix
testsuite/AdResS/MTSAdResS/test_MTSAdResS.py on lines 214..258

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 646.

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_fixed_sphere(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.0, 5.5, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(5.0, 6.5, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 1 other location - About 5 days to fix
testsuite/AdResS/TDforce/test_TDforce.py on lines 43..94

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 594.

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_slab(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.5, 5.0, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.5, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/TDforce/test_TDforce.py and 1 other location - About 5 days to fix
testsuite/AdResS/TDforce/test_TDforce.py on lines 96..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 594.

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_potential_decoupling(self):
        #add particles
        particle_list = [
            (4, 1,  0, espressopp.Real3D(2.0, 2.0, 2.0), 1.0, 0),
            (5, 1,  0, espressopp.Real3D(2.3, 2.0, 2.0), 1.0, 0),
Severity: Major
Found in testsuite/thermo_integration/testThermoIntegration.py and 1 other location - About 5 days to fix
testsuite/thermo_integration/testThermoIntegration.py on lines 86..128

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 534.

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_potential_annihilation(self):
        #add particles
        particle_list = [
            (4, 1,  0, espressopp.Real3D(2.0, 2.0, 2.0), 1.0, 0),
            (5, 1,  0, espressopp.Real3D(2.3, 2.0, 2.0), 1.0, 0),
Severity: Major
Found in testsuite/thermo_integration/testThermoIntegration.py and 1 other location - About 5 days to fix
testsuite/thermo_integration/testThermoIntegration.py on lines 42..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 534.

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_span_false(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/RDFatomistic/test_RDFatomistic.py and 1 other location - About 3 days to fix
testsuite/AdResS/RDFatomistic/test_RDFatomistic.py on lines 40..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 400.

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_span_true(self):
        # add some particles
        particle_list = [
            (1, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 0),
            (2, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 1.0, 0),
Severity: Major
Found in testsuite/AdResS/RDFatomistic/test_RDFatomistic.py and 1 other location - About 3 days to fix
testsuite/AdResS/RDFatomistic/test_RDFatomistic.py on lines 77..112

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 400.

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 readimptypes:
                if line.strip() == "" or '[' in line: # end of impropertypes section
                    readimptypes = False
                else:
                    tmp = line.split()
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 3 days to fix
src/tools/gromacs.py on lines 411..438

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 391.

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 readdhtypes:
                if line.strip() == "" or '[' in line: # end of dihedraltypes section
                    readdhtypes = False
                else:
                    tmp = line.split()
Severity: Major
Found in src/tools/gromacs.py and 1 other location - About 3 days to fix
src/tools/gromacs.py on lines 385..409

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 391.

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 pidCG in range(num_particles_CG):

    # we put CG molecule in first atom, later CG molecules will be positioned in the center
    # note that we put the CG molecule at the first atom's position. Later the CG molecule will be positioned in the center of mass of all it's atoms
    tmptuple = [pidCG+num_particles_AT+1]
Severity: Major
Found in examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py and 1 other location - About 3 days to fix
examples/adress/hadress_water/water.py on lines 120..151

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

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