From 7ea366b3ced9b66d08ece6cb86c7ec6cb64b33fc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 19:42:40 -0500 Subject: [PATCH 1/3] fix formatting issue --- doc/src/Commands_bond.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 8e43605c80..27ff2d19da 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -13,7 +13,7 @@ .. _bond: -bond_style potentials +Bond_style potentials ===================== All LAMMPS :doc:`bond_style ` commands. Some styles have @@ -51,7 +51,7 @@ OPT. .. _angle: -angle_style potentials +Angle_style potentials ====================== All LAMMPS :doc:`angle_style ` commands. Some styles have @@ -93,7 +93,7 @@ OPT. .. _dihedral: -dihedral_style potentials +Dihedral_style potentials ========================= All LAMMPS :doc:`dihedral_style ` commands. Some styles @@ -132,7 +132,7 @@ OPT. .. _improper: -improper_style potentials +Improper_style potentials ========================= All LAMMPS :doc:`improper\_style ` commands. Some styles From 019c70140fd735b8f9fcc406abeb9af98dfe2ac1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 19:43:00 -0500 Subject: [PATCH 2/3] add and correct kspace style entries --- doc/src/Commands_kspace.rst | 10 +++++++--- doc/src/kspace_style.rst | 27 ++++++++++++++++----------- 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index fc2418ecf7..3a23520171 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -24,12 +24,16 @@ OPT. * :doc:`ewald (o) ` * :doc:`ewald/disp ` + * :doc:`ewald/dipole ` + * :doc:`ewald/dipole/spin ` * :doc:`msm (o) ` * :doc:`msm/cg (o) ` - * :doc:`pppm (gok) ` + * :doc:`pppm (giko) ` * :doc:`pppm/cg (o) ` - * :doc:`pppm/disp (i) ` - * :doc:`pppm/disp/tip4p ` + * :doc:`pppm/dipole ` + * :doc:`pppm/dipole/spin ` + * :doc:`pppm/disp (io) ` + * :doc:`pppm/disp/tip4p (o) ` * :doc:`pppm/stagger ` * :doc:`pppm/tip4p (o) ` * :doc:`scafacos ` diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index b5c649a885..c35e38d1db 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -11,26 +11,30 @@ Syntax kspace_style style value -* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos* +* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos* .. parsed-literal:: *none* value = none *ewald* value = accuracy accuracy = desired relative error in forces - *ewald/disp* value = accuracy - accuracy = desired relative error in forces - *ewald/omp* value = accuracy - accuracy = desired relative error in forces *ewald/dipole* value = accuracy accuracy = desired relative error in forces *ewald/dipole/spin* value = accuracy accuracy = desired relative error in forces + *ewald/disp* value = accuracy + accuracy = desired relative error in forces + *ewald/omp* value = accuracy + accuracy = desired relative error in forces *pppm* value = accuracy accuracy = desired relative error in forces *pppm/cg* values = accuracy (smallq) accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) + *pppm/dipole* value = accuracy + accuracy = desired relative error in forces + *pppm/dipole/spin* value = accuracy + accuracy = desired relative error in forces *pppm/disp* value = accuracy accuracy = desired relative error in forces *pppm/tip4p* value = accuracy @@ -41,22 +45,23 @@ Syntax accuracy = desired relative error in forces *pppm/intel* value = accuracy accuracy = desired relative error in forces + *pppm/disp/intel* value = accuracy + accuracy = desired relative error in forces *pppm/kk* value = accuracy accuracy = desired relative error in forces *pppm/omp* value = accuracy accuracy = desired relative error in forces - *pppm/cg/omp* value = accuracy + *pppm/cg/omp* values = accuracy (smallq) accuracy = desired relative error in forces - *pppm/disp/intel* value = accuracy + smallq = cutoff for charges to be considered (optional) (charge units) + *pppm/disp/omp* value = accuracy accuracy = desired relative error in forces *pppm/tip4p/omp* value = accuracy accuracy = desired relative error in forces + *pppm/disp/tip4p/omp* value = accuracy + accuracy = desired relative error in forces *pppm/stagger* value = accuracy accuracy = desired relative error in forces - *pppm/dipole* value = accuracy - accuracy = desired relative error in forces - *pppm/dipole/spin* value = accuracy - accuracy = desired relative error in forces *msm* value = accuracy accuracy = desired relative error in forces *msm/cg* value = accuracy (smallq) From 05b68d9e0d6ab24b6915d8af3806543bd580cb0f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 19:43:29 -0500 Subject: [PATCH 3/3] add missing pair style entries --- doc/src/Commands_pair.rst | 8 ++++++++ doc/src/pair_style.rst | 2 +- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index eaf0e680a0..23765c84f6 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -198,10 +198,17 @@ OPT. * :doc:`oxdna2/hbond ` * :doc:`oxdna2/stk ` * :doc:`oxdna2/xstk ` + * :doc:`oxrna2/excv ` + * :doc:`oxrna2/hbond ` + * :doc:`oxrna2/dh ` + * :doc:`oxrna2/stk ` + * :doc:`oxrna2/xstk ` + * :doc:`oxrna2/coaxstk ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` * :doc:`peri/ves ` + * :doc:`polymorphic ` * :doc:`python ` * :doc:`quip ` * :doc:`reax/c (ko) ` @@ -250,3 +257,4 @@ OPT. * :doc:`yukawa/colloid (go) ` * :doc:`zbl (gko) ` * + * diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index db3056ed64..84548720c0 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -245,7 +245,7 @@ accelerated styles exist. * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term * :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential * :doc:`mie/cut ` - Mie potential -* :doc:`mm3/switch3/coulgauss/long `_ - smoothed MM3 vdW potential with Gaussian electrostatics +* :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field * :doc:`morse ` - Morse potential * :doc:`morse/smooth/linear ` - linear smoothed Morse potential