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examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py

Summary

Maintainability
F
4 days
Test Coverage

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

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

for pid in range(num_particles_AT):
    part = [pid + 1, Real3D(x[pid], y[pid], z[pid]),
            Real3D(vx[pid],vy[pid], vz[pid]), Real3D(0, 0, 0),
            types[pid], masses[pid], charges[pid], 1]
    allParticlesAT.append(part)
Severity: Major
Found in examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py and 1 other location - About 7 hrs to fix
examples/adress/hadress_water/water.py on lines 111..115

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 111.

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 6 locations. Consider refactoring.
Open

verletlist = espressopp.VerletListAdress(system, cutoff=interaction_cutoff_cg, adrcut=interaction_cutoff_verletlist_at,
                                         dEx=ex_size, dHy=hy_size, adrCenter=[Lx/2, Ly/2, Lz/2])
Severity: Major
Found in examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py and 5 other locations - About 1 hr to fix
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressDensityFEC.py on lines 151..153
examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py on lines 150..152
examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py on lines 144..146
examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py on lines 146..148
examples/adress/hadress_water/water.py on lines 101..103

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 49.

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

    outfile.write(fmt%((i+1)*steps*multistep/check*timestep, temp, E_bonds, E_angles, E_nonbonded, E_kinetic, E_total))
Severity: Major
Found in examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py and 1 other location - About 1 hr to fix
examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py on lines 288..288

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 45.

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

    print((fmt%((i+1)*steps*multistep/check*timestep, temp, E_bonds, E_angles, E_nonbonded, E_kinetic, E_total)))
Severity: Major
Found in examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py and 1 other location - About 1 hr to fix
examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py on lines 287..287

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 45.

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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