From dfa2114913705207ddf932ef753859cf46dfa851 Mon Sep 17 00:00:00 2001 From: David van der Spoel Date: Wed, 13 Feb 2019 20:13:58 +0100 Subject: [PATCH] Precision fix for rescbt code. The compute_restangles function was not sufficiently precise. In fact it return completely different results in single and double precision. By making part of the function work in double the issue is fixed. New tests added. Part of #2795 Fixes #2862 Change-Id: Iad7f2bc45be996ba3e16358aab838c5427b157b8 --- src/gromacs/listed_forces/bonded.cpp | 14 +-- src/gromacs/listed_forces/restcbt.cpp | 18 +-- src/gromacs/listed_forces/restcbt.h | 2 +- src/gromacs/listed_forces/tests/bonded.cpp | 4 +- .../Restraints_ListedForcesTest_Ifunc_36.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_37.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_38.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_39.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_40.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_41.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_42.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_43.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_44.xml | 38 +++++++ .../Restraints_ListedForcesTest_Ifunc_45.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_46.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_47.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_48.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_49.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_50.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_51.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_52.xml | 104 ++++++++++++++++++ .../Restraints_ListedForcesTest_Ifunc_53.xml | 104 ++++++++++++++++++ 22 files changed, 1298 insertions(+), 18 deletions(-) create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_36.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_37.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_38.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_39.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_40.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_41.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_42.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_43.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_44.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_45.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_46.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_47.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_48.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_49.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_50.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_51.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_52.xml create mode 100644 src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_53.xml diff --git a/src/gromacs/listed_forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp index 8c03e0a29a..7c4f176ee8 100644 --- a/src/gromacs/listed_forces/bonded.cpp +++ b/src/gromacs/listed_forces/bonded.cpp @@ -2429,13 +2429,13 @@ real restrangles(int nbonds, const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd, int gmx_unused *global_atom_index) { - int i, d, ai, aj, ak, type, m; - int t1, t2; - real v, vtot; - ivec jt, dt_ij, dt_kj; - rvec f_i, f_j, f_k; - real prefactor, ratio_ante, ratio_post; - rvec delta_ante, delta_post, vec_temp; + int i, d, ai, aj, ak, type, m; + int t1, t2; + real v, vtot; + ivec jt, dt_ij, dt_kj; + rvec f_i, f_j, f_k; + double prefactor, ratio_ante, ratio_post; + rvec delta_ante, delta_post, vec_temp; vtot = 0.0; for (i = 0; (i < nbonds); ) diff --git a/src/gromacs/listed_forces/restcbt.cpp b/src/gromacs/listed_forces/restcbt.cpp index 6e88355ff2..01d0a67ea5 100644 --- a/src/gromacs/listed_forces/restcbt.cpp +++ b/src/gromacs/listed_forces/restcbt.cpp @@ -60,15 +60,17 @@ void compute_factors_restangles(int type, const t_iparams forceparams[], rvec delta_ante, rvec delta_post, - real *prefactor, real *ratio_ante, real *ratio_post, real *v) + double *prefactor, double *ratio_ante, double *ratio_post, real *v) { - real theta_equil, k_bending; - real cosine_theta_equil; - real c_ante, c_cros, c_post; - real norm; - real delta_cosine, cosine_theta; - real sine_theta_sq; - real term_theta_theta_equil; + // These variables are double to make the code + // reproducible. + double theta_equil, k_bending; + double cosine_theta_equil; + double c_ante, c_cros, c_post; + double norm; + double delta_cosine, cosine_theta; + double sine_theta_sq; + double term_theta_theta_equil; k_bending = forceparams[type].harmonic.krA; theta_equil = forceparams[type].harmonic.rA*DEG2RAD; diff --git a/src/gromacs/listed_forces/restcbt.h b/src/gromacs/listed_forces/restcbt.h index 56dca730fe..6670abd2e0 100644 --- a/src/gromacs/listed_forces/restcbt.h +++ b/src/gromacs/listed_forces/restcbt.h @@ -79,7 +79,7 @@ void compute_factors_restangles(int type, const t_iparams forceparams[], rvec delta_ante, rvec delta_post, - real *prefactor, real *ratio_ante, real *ratio_post, real *v); + double *prefactor, double *ratio_ante, double *ratio_post, real *v); /*! \brief Compute factors for restricted dihedral potentials. diff --git a/src/gromacs/listed_forces/tests/bonded.cpp b/src/gromacs/listed_forces/tests/bonded.cpp index a2f0158389..80cbd03d05 100644 --- a/src/gromacs/listed_forces/tests/bonded.cpp +++ b/src/gromacs/listed_forces/tests/bonded.cpp @@ -660,8 +660,8 @@ std::vector c_InputRestraints = { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRES, -105.0, 15.0, 2) }, { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRESZ, -100.0, 10.0, 2, -80.0, 20.0) }, { iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRESZ, -105.0, 15.0, 2) }, - //{ iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0) }, - //{ iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0, 110.0, 45.0) } + { iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0) }, + { iListInput(2e-3, 1e-8).setHarmonic(F_RESTRANGLES, 100.0, 50.0, 110.0, 45.0) } }; //! Coordinates for testing diff --git a/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_36.xml b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_36.xml new file mode 100644 index 0000000000..458842ddeb --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_36.xml @@ -0,0 +1,38 @@ + + + + + + 13793.486079955308 + 0 + + -7.1054273576010019e-15 + 5.6843418860808015e-14 + -7.6833543971588369e-09 + + + 4 + + -2761787.8827562206 + 0 + 0 + + + -2748083.9432400633 + 643.09135302869788 + -275493.59129982314 + + + 5509923.1808657609 + -963.09638345872963 + 275170.50497721677 + + + -51.354869477236797 + 320.00503043003181 + 323.08632259866607 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_37.xml b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_37.xml new file mode 100644 index 0000000000..458842ddeb --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_37.xml @@ -0,0 +1,38 @@ + + + + + + 13793.486079955308 + 0 + + -7.1054273576010019e-15 + 5.6843418860808015e-14 + -7.6833543971588369e-09 + + + 4 + + -2761787.8827562206 + 0 + 0 + + + -2748083.9432400633 + 643.09135302869788 + -275493.59129982314 + + + 5509923.1808657609 + -963.09638345872963 + 275170.50497721677 + + + -51.354869477236797 + 320.00503043003181 + 323.08632259866607 + + + + + diff --git a/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_38.xml b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_38.xml new file mode 100644 index 0000000000..458842ddeb --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_38.xml @@ -0,0 +1,38 @@ + + + + + + 13793.486079955308 + 0 + + -7.1054273576010019e-15 + 5.6843418860808015e-14 + -7.6833543971588369e-09 + + + 4 + + -2761787.8827562206 + 0 + 0 + + + -2748083.9432400633 + 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a/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_51.xml b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_51.xml new file mode 100644 index 0000000000..287aca83f4 --- /dev/null +++ b/src/gromacs/listed_forces/tests/refdata/Restraints_ListedForcesTest_Ifunc_51.xml @@ -0,0 +1,104 @@ + + + + + + + 181.72792025950673 + 0 + + 4.5474735088646412e-13 + -4.5474735088646412e-13 + 0 + + + 4 + + 105.65070375739712 + -168.65747820489509 + 0 + + + -3076.5687111064121 + -5986.1289531038201 + 0 + + + -336.58711384843497 + 3364.8371236971734 + 0 + + + 3307.5051211974505 + 2789.9493076115414 + 0 + + + + + 181.72792025950673 + 0 + + 4.5474735088646412e-13 + -4.5474735088646412e-13 + 0 + + + 4 + + 105.65070375739712 + -168.65747820489509 + 0 + + + -3076.5687111064121 + -5986.1289531038201 + 0 + + + -336.58711384843497 + 3364.8371236971734 + 0 + + + 3307.5051211974505 + 2789.9493076115414 + 0 + + + + + 181.72792025950673 + 0 + + 4.5474735088646412e-13 + 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