Loading doc/src/angle_class2.txt +1 −1 Original line number Diff line number Diff line Loading @@ -7,8 +7,8 @@ :line angle_style class2 command :h3 angle_style class2/omp command :h3 angle_style class2/kk command :h3 angle_style class2/omp command :h3 angle_style class2/p6 command :h3 [Syntax:] Loading doc/src/angle_style.txt +12 −12 Original line number Diff line number Diff line Loading @@ -68,20 +68,20 @@ doc page. "charmm"_angle_charmm.html - CHARMM angle "class2"_angle_class2.html - COMPASS (class 2) angle "class2/p6"_angle_class2.html - "cosine"_angle_cosine.html - cosine angle potential "cosine/buck6d"_angle_cosine_buck6d.html - "cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential "class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order "cosine"_angle_cosine.html - angle with cosine term "cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms "cosine/delta"_angle_cosine_delta.html - angle with difference of cosines "cosine/periodic"_angle_cosine_periodic.html - DREIDING angle "cosine/shift"_angle_cosine_shift.html - "cosine/shift/exp"_angle_cosine_shift_exp.html - "cosine/squared"_angle_cosine_squared.html - cosine squared angle potential "dipole"_angle_dipole.html - "fourier"_angle_fourier.html - "fourier/simple"_angle_fourier_simple.html - "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term "dipole"_angle_dipole.html - angle that controls orientation of a point dipole "fourier"_angle_fourier.html - angle with multiple cosine terms "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term "harmonic"_angle_harmonic.html - harmonic angle "quartic"_angle_quartic.html - "sdk"_angle_sdk.html - "quartic"_angle_quartic.html - angle with cubic and quartic terms "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms "table"_angle_table.html - tabulated by angle :ul :line Loading doc/src/bond_style.txt +5 −5 Original line number Diff line number Diff line Loading @@ -76,14 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "class2"_bond_class2.html - COMPASS (class 2) bond "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles "gromos"_bond_gromos.html - "gromos"_bond_gromos.html - GROMOS force field bond "harmonic"_bond_harmonic.html - harmonic bond "harmonic/shift"_bond_harmonic_shift.html - "harmonic/shift/cut"_bond_harmonic_shift_cut.html - "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond "oxdna/fene"_bond_oxdna.html - "oxdna2/fene"_bond_oxdna.html - "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling "oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul Loading doc/src/dihedral_style.txt +9 −9 Original line number Diff line number Diff line Loading @@ -90,19 +90,19 @@ doc page. "hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul "charmm"_dihedral_charmm.html - CHARMM dihedral "charmmfsw"_dihedral_charmm.html - "charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching "class2"_dihedral_class2.html - COMPASS (class 2) dihedral "cosine/shift/exp"_dihedral_cosine_shift_exp.html - "fourier"_dihedral_fourier.html - "cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant "fourier"_dihedral_fourier.html - dihedral with multiple cosine terms "harmonic"_dihedral_harmonic.html - harmonic dihedral "helix"_dihedral_helix.html - helix dihedral "multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral "nharmonic"_dihedral_nharmonic.html - "multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms "nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms "opls"_dihedral_opls.html - OPLS dihedral "quadratic"_dihedral_quadratic.html - "spherical"_dihedral_spherical.html - "table"_dihedral_table.html - "table/cut"_dihedral_table_cut.html - :ul "quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle "spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities "table"_dihedral_table.html - tabulated dihedral "table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul :line Loading doc/src/improper_style.txt +5 −5 Original line number Diff line number Diff line Loading @@ -69,13 +69,13 @@ doc page. "hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul "class2"_improper_class2.html - COMPASS (class 2) improper "cossq"_improper_cossq.html - "cossq"_improper_cossq.html - improper with a cosine squared term "cvff"_improper_cvff.html - CVFF improper "distance"_improper_distance.html - "fourier"_improper_fourier.html - "distance"_improper_distance.html - improper based on distance between atom planes "fourier"_improper_fourier.html - improper with multiple cosine terms "harmonic"_improper_harmonic.html - harmonic improper "inversion/harmonic"_improper_inversion_harmonic.html - "ring"_improper_ring.html - "inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition "ring"_improper_ring.html - improper which prevents planar conformations "umbrella"_improper_umbrella.html - DREIDING improper :ul :line Loading Loading
doc/src/angle_class2.txt +1 −1 Original line number Diff line number Diff line Loading @@ -7,8 +7,8 @@ :line angle_style class2 command :h3 angle_style class2/omp command :h3 angle_style class2/kk command :h3 angle_style class2/omp command :h3 angle_style class2/p6 command :h3 [Syntax:] Loading
doc/src/angle_style.txt +12 −12 Original line number Diff line number Diff line Loading @@ -68,20 +68,20 @@ doc page. "charmm"_angle_charmm.html - CHARMM angle "class2"_angle_class2.html - COMPASS (class 2) angle "class2/p6"_angle_class2.html - "cosine"_angle_cosine.html - cosine angle potential "cosine/buck6d"_angle_cosine_buck6d.html - "cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential "class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order "cosine"_angle_cosine.html - angle with cosine term "cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms "cosine/delta"_angle_cosine_delta.html - angle with difference of cosines "cosine/periodic"_angle_cosine_periodic.html - DREIDING angle "cosine/shift"_angle_cosine_shift.html - "cosine/shift/exp"_angle_cosine_shift_exp.html - "cosine/squared"_angle_cosine_squared.html - cosine squared angle potential "dipole"_angle_dipole.html - "fourier"_angle_fourier.html - "fourier/simple"_angle_fourier_simple.html - "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term "dipole"_angle_dipole.html - angle that controls orientation of a point dipole "fourier"_angle_fourier.html - angle with multiple cosine terms "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term "harmonic"_angle_harmonic.html - harmonic angle "quartic"_angle_quartic.html - "sdk"_angle_sdk.html - "quartic"_angle_quartic.html - angle with cubic and quartic terms "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms "table"_angle_table.html - tabulated by angle :ul :line Loading
doc/src/bond_style.txt +5 −5 Original line number Diff line number Diff line Loading @@ -76,14 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "class2"_bond_class2.html - COMPASS (class 2) bond "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles "gromos"_bond_gromos.html - "gromos"_bond_gromos.html - GROMOS force field bond "harmonic"_bond_harmonic.html - harmonic bond "harmonic/shift"_bond_harmonic_shift.html - "harmonic/shift/cut"_bond_harmonic_shift_cut.html - "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond "oxdna/fene"_bond_oxdna.html - "oxdna2/fene"_bond_oxdna.html - "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling "oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul Loading
doc/src/dihedral_style.txt +9 −9 Original line number Diff line number Diff line Loading @@ -90,19 +90,19 @@ doc page. "hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul "charmm"_dihedral_charmm.html - CHARMM dihedral "charmmfsw"_dihedral_charmm.html - "charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching "class2"_dihedral_class2.html - COMPASS (class 2) dihedral "cosine/shift/exp"_dihedral_cosine_shift_exp.html - "fourier"_dihedral_fourier.html - "cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant "fourier"_dihedral_fourier.html - dihedral with multiple cosine terms "harmonic"_dihedral_harmonic.html - harmonic dihedral "helix"_dihedral_helix.html - helix dihedral "multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral "nharmonic"_dihedral_nharmonic.html - "multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms "nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms "opls"_dihedral_opls.html - OPLS dihedral "quadratic"_dihedral_quadratic.html - "spherical"_dihedral_spherical.html - "table"_dihedral_table.html - "table/cut"_dihedral_table_cut.html - :ul "quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle "spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities "table"_dihedral_table.html - tabulated dihedral "table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul :line Loading
doc/src/improper_style.txt +5 −5 Original line number Diff line number Diff line Loading @@ -69,13 +69,13 @@ doc page. "hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul "class2"_improper_class2.html - COMPASS (class 2) improper "cossq"_improper_cossq.html - "cossq"_improper_cossq.html - improper with a cosine squared term "cvff"_improper_cvff.html - CVFF improper "distance"_improper_distance.html - "fourier"_improper_fourier.html - "distance"_improper_distance.html - improper based on distance between atom planes "fourier"_improper_fourier.html - improper with multiple cosine terms "harmonic"_improper_harmonic.html - harmonic improper "inversion/harmonic"_improper_inversion_harmonic.html - "ring"_improper_ring.html - "inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition "ring"_improper_ring.html - improper which prevents planar conformations "umbrella"_improper_umbrella.html - DREIDING improper :ul :line Loading
