0000035: Too Much Pi - MantisBT

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ID

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Date Submitted

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0000035

Rosetta

[All Projects] Bad Coding

public

2012-07-02 17:42

2012-09-20 13:41

Reporter

renfrew

Assigned To

honda

Priority

low

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

All platforms

OS

Any

OS Version

Any

Product Version

Trunk

Fixed in Version

Trunk

Summary

0000035: Too Much Pi

Description

Few people use the constants in NumericTraits and this has resulted in many different definitions of pi. I suspect that changing all of these will affect the integration tests. There may be additional numerical constants that have been abused in this manner.

Additional Information

src/apps/pilot/chrisk/pep_prep.cc: Real pi( 3.14159 );
src/apps/pilot/chrisk/pepspec_anchor_dock.cc: Real pi( 3.14159 );
src/apps/pilot/frank/cryst_design.cc: core::Real deg2rad = 3.14159265/180.0;
src/apps/pilot/lemmon/deepMove.cc: core::Real const radians=3.14159;// not sure if this is degree or radians
src/apps/pilot/ragul/ragul_small_mol_map.cc:#define PI 3.14159265
src/apps/pilot/rhiju/rna_protein_test.cc: Real const phi = uniform() * 2 * 3.141592654;
src/apps/pilot/sergey/GA.cc: const Real PI = 3.141592653589;
src/apps/pilot/will/crossmatch.cc: Real ang1 = 180.0-acos(max(-1.0,min(1.0,mi2.axis .dot( mi1.axis ))))*180.0/3.14159;
src/apps/pilot/will/crossmatch.cc: Real ang2 = -acos(max(-1.0,min(1.0,mi2.ortho.dot(rotation_matrix_degrees(axis,ang1)*mi1.ortho))))*180.0/3.14159;
src/apps/pilot/will/crossmatch_d2.cc: Real ang1 = 180.0-acos(max(-1.0,min(1.0,mi2.axis .dot( mi1.axis ))))*180.0/3.14159;
src/apps/pilot/will/crossmatch_d2.cc: Real ang2 = -acos(max(-1.0,min(1.0,mi2.ortho.dot(rotation_matrix_degrees(axis,ang1)*mi1.ortho))))*180.0/3.14159;
src/apps/pilot/will/dubois.cc: pose.set_dof(core::id::DOF_ID(core::id::AtomID(6,2),core::id::THETA),3.14159);
src/apps/pilot/will/dubois.cc: pose.set_dof(core::id::DOF_ID(core::id::AtomID(6,2),core::id::THETA),3.14159);
src/apps/pilot/will/dubois.cc: pose.set_dof(id::DOF_ID(id::AtomID(6,2),id::THETA),3.14159);
src/apps/pilot/will/dubois.cc: pose.set_dof(id::DOF_ID(id::AtomID(6,2),id::THETA),3.14159);
src/apps/pilot/will/dubois.cc: pose.set_dof(id::DOF_ID(id::AtomID(6,2),id::THETA),3.14159);
src/apps/pilot/will/gen_cyc_gly_cst.cc: pose.add_constraint(new DihedralConstraint(AtomID(5,1),AtomID(1,1),AtomID(3,N),AtomID(4,N),new core::scoring::constraints::HarmonicFunc(3.14159 ,0.0001)));
src/apps/pilot/will/gen_d2.cc: //hisp.set_dof( DOF_ID(AtomID(11,ir),PHI ), 3.141593);
src/apps/pilot/will/gen_d2_4his.cc: //hisp.set_dof( DOF_ID(AtomID(11,ir),PHI ), 3.141593);
src/apps/pilot/will/gen_disulf_homodimer.cc: cysp.set_dof( DOF_ID(AtomID(11,ir),PHI ), 3.141593);
src/apps/pilot/will/gensym_3bpy_from_dimer.cc: new HarmonicFunc(3.14159,0.1) ) );
src/apps/pilot/will/gensym_3bpy_from_dimer.cc: new HarmonicFunc(3.14159,0.1) ) );
src/apps/pilot/will/gensym_3bpy_from_dimer.cc: new HarmonicFunc(3.14159,0.1) ) );
src/apps/pilot/will/gensym_3bpy_from_dimer.cc: new HarmonicFunc(3.14159,0.1) ) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C2"),5),AtomID(tmp.residue(5).atom_index("C7"),5),AtomID(9,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C7"),5),AtomID(9,1),AtomID(n1a,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C8"),5),AtomID(tmp.residue(5).atom_index("C9"),5),AtomID(9,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C9"),5),AtomID(9,3),AtomID(n2a,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk11,2),AtomID(bk12,2),AtomID(bk13,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk12,2),AtomID(bk13,1),AtomID(bk14,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk21,4),AtomID(bk22,4),AtomID(bk23,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk22,4),AtomID(bk23,3),AtomID(bk24,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp2.add_constraint( new AngleConstraint( AtomID(tmp2.residue(7).nheavyatoms()-2,7), AtomID(tmp2.residue(7).nheavyatoms()-1,7), AtomID(iO1,5), new HarmonicFunc(3.14159*2.0/3.0,0.2)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C2"),r5),AtomID(tmp.residue(5).atom_index("C7"),r5),AtomID(9,r1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C7"),r5),AtomID(9,r1),AtomID(n1a,r1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C8"),r5),AtomID(tmp.residue(5).atom_index("C9"),r5),AtomID(9,r3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C9"),r5),AtomID(9,r3),AtomID(n2a,r3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(bk11,r2),AtomID(bk12,r2),AtomID(bk13,r1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(bk12,r2),AtomID(bk13,r1),AtomID(bk14,r1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(bk21,r4),AtomID(bk22,r4),AtomID(bk23,r3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(bk22,r4),AtomID(bk23,r3),AtomID(bk24,r3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs.cc: tmp3.add_constraint( new AngleConstraint( AtomID(tmp2.residue(7).nheavyatoms()-2 ,r7), AtomID(tmp2.residue(7).nheavyatoms()-1,r7), AtomID(iO1,r5), new HarmonicFunc(3.14159*2.0/3.0,0.05)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C2"),5),AtomID(tmp.residue(5).atom_index("C7"),5),AtomID(9,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C7"),5),AtomID(9,1),AtomID(n1a,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C8"),5),AtomID(tmp.residue(5).atom_index("C9"),5),AtomID(9,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(tmp.residue(5).atom_index("C9"),5),AtomID(9,3),AtomID(n2a,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk11,2),AtomID(bk12,2),AtomID(bk13,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk12,2),AtomID(bk13,1),AtomID(bk14,1), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk21,4),AtomID(bk22,4),AtomID(bk23,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp.add_constraint( new AngleConstraint( AtomID(bk22,4),AtomID(bk23,3),AtomID(bk24,3), new HarmonicFunc(3.14159,0.3)) );
src/apps/pilot/will/test_ikrs2.cc: tmp2.add_constraint( new AngleConstraint( AtomID(tmp2.residue(7).nheavyatoms()-2,7),AtomID(tmp2.residue(7).nheavyatoms()-1,7), AtomID(iO1,5), new HarmonicFunc(3.14159*2.0/3.0,0.2)) );
src/apps/pilot/will/test_leerichards.cc: core::Real mag = uniform() * 2.0 * 3.14159;
src/apps/public/pepspec/pepspec_anchor_dock.cc: Real pi( 3.14159 );
src/core/chemical/orbitals/AssignOrbitals.cc: if( (theta < 1e-2) || (theta > 3.14-1e-2) )
src/core/chemical/orbitals/AssignOrbitals.cc: if( (theta < 1e-2) || (theta > 3.14-1e-2) )
src/core/chemical/ResidueType.cc: if( (theta < 1e-2) || (theta > 3.14-1e-2) )
src/core/coarse/Translator.cc: const Real Pi (3.14159); // EVIL -- use numeric::d::constants
src/core/coarse/Translator.cc: const Real Pi ( 3.14159 ); //EVIL
src/core/scoring/electron_density_atomwise/ElectronDensityAtomwise.cc: const Real PI = 3.1415926;
src/core/scoring/hbonds/hbonds_geom.cc: //std::cout << "penalizing hbond by " << cos2ChiShifted << " for having hydroxyl hydrogen too close: chi " << chi*180/3.1415926535 << std::endl;
src/core/scoring/methods/GaussianOverlapEnergy.cc: score = ((sqrt(3.14158)*r1*r2)/(sqrt(r1*r1+r2*r2)))*(exp(-d2/(r1*r1+r2*r2)));
src/core/scoring/packstat/compute_sasa.cc: PackstatReal mag = uniform() * 2 * 3.14159;
src/core/scoring/packstat/compute_sasa.cc: return alpha*alpha*3.14159;
src/core/scoring/packstat/LeeRichards.cc: // a->circle->dr += fabs(a->start_angle-a->end_angle);///180.0*3.14159265;
src/core/scoring/packstat/packing_score_params.cc: p.weight(1,23) = -0.00723770034705824; p.center(1,23) = 3.14094836962294;
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+2]=2.0*3.1415*numeric::random::uniform();//alpha
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+3]=2.0*3.1415*numeric::random::uniform();//beta
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+4]=2.0*3.1415*numeric::random::uniform();//gamma
src/core/scoring/ResidualDipolarCoupling.cc: tr.Trace << "alpha: " << par[ex*n_par+2]*180/3.1415926<< std::endl;
src/core/scoring/ResidualDipolarCoupling.cc: tr.Trace << "beta: " << par[ex*n_par+3]*180/3.1415926<< std::endl;
src/core/scoring/ResidualDipolarCoupling.cc: tr.Trace << "gamma:" << par[ex*n_par+4]*180/3.1415926<< std::endl;
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+1]=2.0*3.1415*numeric::random::uniform();//alpha
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+2]=2.0*3.1415*numeric::random::uniform();//beta
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+3]=2.0*3.1415*numeric::random::uniform();//gamma
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+1]=2.0*3.1415*numeric::random::uniform();//alpha
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+2]=2.0*3.1415*numeric::random::uniform();//beta
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+3]=2.0*3.1415*numeric::random::uniform();//gamma
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+0]=2.0*3.1415*numeric::random::uniform();//alpha
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+1]=2.0*3.1415*numeric::random::uniform();//beta
src/core/scoring/ResidualDipolarCoupling.cc: par[ex*n_par+2]=2.0*3.1415*numeric::random::uniform();//gamma
src/core/scoring/SecondaryStructurePotential.cc: rsigma_dot( 5, 14, 1, 1 ) = -3.149200;
src/devel/path_rover/pathrover.cc:#define PI 3.141592653 // TODO: use numeric
src/devel/path_rover/pathrover_partial_data_manager.cc: angle = (angle>0.0) ? 3.14159265359-angle : -(3.14159265359+angle);
src/devel/path_rover/pathrover_partial_data_manager.cc: angle = angle*180/3.14159265359;
src/devel/path_rover/pathrover_partial_data_manager.hh://#define [^] M_PI 3.14159265359
src/numeric/kinematic_closure/bridgeObjects.cc:#define pi 3.14159265358979323846264338327950288
src/protocols/abinitio/vs_test.cc: log << F( 8, 3, 3.14159 ) << std::endl;
src/protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.cc: rsigma_dot( 5, 14, 1, 1 ) = -3.149200;
src/protocols/fldsgn/potentials/sspot/SSPairPotential.cc: rsigma_dot( 5, 14, 1, 1 ) = -3.149200;
src/protocols/fldsgn/topology/Sheet.cc:#define PI 3.141592
src/protocols/frag_picker/scores/InterbondAngleScore.cc: double angle = angle_of(v1, v2)*180.0/3.14159;
src/protocols/sparta/constants.hh:#define SPARTA_PI 3.14159265358979323846
src/protocols/swa/rna/StepWiseRNA_FloatingBase_Sampler_Util.hh:#define PI 3.14159265
src/protocols/viewer/viewers.cc: 0.5 * ( - cos( 3.14159 * p ) + 1.0 );
src/protocols/viewer/viewers.cc: 0.5 * ( cos( 3.14159 * p ) + 1.0 );

Tags

No tags attached.

Application(s) Affected

All

Command Line Used

NA

Developer Options

Fixed in SVN Version

51160 + 51165

Relationships

Notes
(0000021) smlewis (Administrator) 2012-07-02 18:10	I'm going to close this as a dup of #314159

(0000024) delucasl (Administrator) 2012-07-09 14:55 edited on: 2012-07-09 14:56	Is there a conceivable case in which an integration test caused by changing "3.14159" to the standard numeric constant would be actually detrimental to the scientific results? Edit: I suppose if the reduced accuracy had in some way been optimized around.

(0000025) renfrew (Developer) 2012-07-09 15:12	I suspect that there would be little difference scientifically. Probably just trajectory changes integration tests. Most of the examples above are from people setting HarmonicConstraints on dihedral angles. The HarmonicConstraints are in radians and people want to constrain them to 180 degrees (1 PI radians). Its really just magic number cleanup.

(0000098) honda (Developer) 2012-09-14 18:02	May cause numerical differences in some architectures. Affected files: core/chemical/ResidueType.cc core/chemical/orbitals/AssignOrbitals.cc core/coarse/Translator.cc core/scoring/ResidualDipolarCoupling.cc core/scoring/methods/GaussianOverlapEnergy.cc core/scoring/packstat/compute_sasa.cc protocols/swa/rna/StepWise* protocols/frag_picker/scores/InterboundAngleScore.cc protocols/viewer/viewers.cc protocols/fldsgn/topology/Sheet.cc protocols/sparta/* devel/path_rover/* apps/public/pepspec/pepspec_anchor_dock.cc apps/pilot/chrisk/* apps/pilot/lemmon/deepMove.cc apps/pilot/rhiju/rna_protein_test.cc apps/pilot/will/* apps/pilot/sergey/GA.cc apps/pilot/frank/cryst_design.cc apps/pilot/ragul/ragul_small_mol_map.cc

Issue History
Date Modified	Username	Field	Change
2012-07-02 17:42	renfrew	New Issue
2012-07-02 18:10	smlewis	Note Added: 0000021
2012-07-09 14:55	delucasl	Note Added: 0000024
2012-07-09 14:56	delucasl	Note Edited: 0000024	View Revisions
2012-07-09 15:12	renfrew	Note Added: 0000025
2012-08-04 14:13	Labonte	Assigned To	=> Labonte
2012-08-04 14:13	Labonte	Status	new => assigned
2012-08-27 17:02	smlewis	Assigned To	Labonte => honda
2012-09-14 18:02	honda	Fixed in SVN Version	=> 51160
2012-09-14 18:02	honda	Note Added: 0000098
2012-09-14 18:02	honda	Resolution	open => fixed
2012-09-14 18:02	honda	Fixed in Version	=> Trunk
2012-09-20 11:25	honda	Status	assigned => closed
2012-09-20 13:41	smlewis	Fixed in SVN Version	51160 => 51160 + 51165
2012-09-20 13:41	smlewis	Status	closed => resolved

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