Merge pull request lammps#4030 from alphataubio/alphataubio-charmmfsw-kk

Kokkos charmmfsw pair and dihedral styles
akohlmey · Jan 18, 2024 · 54794a4 · 54794a4
2 parents af60285 + 4b561d5
commit 54794a4
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diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
@@ -124,7 +124,7 @@ OPT.
    *
    *
    * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`charmmfsw (k) <dihedral_charmm>`
    * :doc:`class2 (ko) <dihedral_class2>`
    * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
    * :doc:`fourier (io) <dihedral_fourier>`

diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
@@ -146,7 +146,7 @@ OPT.
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
    * :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
-   * :doc:`lj/charmmfsw/coul/long <pair_charmm>`
+   * :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
    * :doc:`lj/class2 (gko) <pair_class2>`
    * :doc:`lj/class2/coul/cut (ko) <pair_class2>`
    * :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst
@@ -70,7 +70,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`angle_coeff <angle_coeff>`
+:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`dihedral_style charmm <dihedral_charmm>`,
+:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst
@@ -3,6 +3,7 @@
 .. index:: dihedral_style charmm/kk
 .. index:: dihedral_style charmm/omp
 .. index:: dihedral_style charmmfsw
+.. index:: dihedral_style charmmfsw/kk
 
 dihedral_style charmm command
 =============================
@@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
 dihedral_style charmmfsw command
 ================================
 
+Accelerator Variants: *charmmfsw/kk*
+
 Syntax
 """"""
 
@@ -144,7 +147,9 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`dihedral_coeff <dihedral_coeff>`
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`pair_style lj/charmm variants <pair_charmm>`,
+:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst
@@ -376,7 +376,7 @@ not listed, the default diameter of each atom in the molecule is 1.0.
 
 ----------
 
-..versionadded:: TBD
+.. versionadded:: TBD
 
 *Dipoles* section:
 

diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst
@@ -16,6 +16,7 @@
 .. index:: pair_style lj/charmm/coul/msm/omp
 .. index:: pair_style lj/charmmfsw/coul/charmmfsh
 .. index:: pair_style lj/charmmfsw/coul/long
+.. index:: pair_style lj/charmmfsw/coul/long/kk
 
 pair_style lj/charmm/coul/charmm command
 ========================================
@@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
 pair_style lj/charmmfsw/coul/long command
 =========================================
 
+Accelerator Variants: *lj/charmmfsw/coul/long/kk*
+
 Syntax
 """"""
 
@@ -281,7 +284,9 @@ page for more info.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
+:doc:`dihedral_style charmm <dihedral_charmm>`,
+:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
 
 Default
 """""""

diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
@@ -106,6 +106,8 @@ action compute_temp_kokkos.cpp
 action compute_temp_kokkos.h
 action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp
 action dihedral_charmm_kokkos.h dihedral_charmm.h
+action dihedral_charmmfsw_kokkos.cpp dihedral_charmmfsw.cpp
+action dihedral_charmmfsw_kokkos.h dihedral_charmmfsw.h
 action dihedral_class2_kokkos.cpp dihedral_class2.cpp
 action dihedral_class2_kokkos.h dihedral_class2.h
 action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp
@@ -310,6 +312,8 @@ action pair_lj_charmm_coul_charmm_kokkos.cpp pair_lj_charmm_coul_charmm.cpp
 action pair_lj_charmm_coul_charmm_kokkos.h pair_lj_charmm_coul_charmm.h
 action pair_lj_charmm_coul_long_kokkos.cpp pair_lj_charmm_coul_long.cpp
 action pair_lj_charmm_coul_long_kokkos.h pair_lj_charmm_coul_long.h
+action pair_lj_charmmfsw_coul_long_kokkos.cpp pair_lj_charmmfsw_coul_long.cpp
+action pair_lj_charmmfsw_coul_long_kokkos.h pair_lj_charmmfsw_coul_long.h
 action pair_lj_class2_coul_cut_kokkos.cpp pair_lj_class2_coul_cut.cpp
 action pair_lj_class2_coul_cut_kokkos.h pair_lj_class2_coul_cut.h
 action pair_lj_class2_coul_long_kokkos.cpp pair_lj_class2_coul_long.cpp

diff --git a/src/KOKKOS/atom_map_kokkos.cpp b/src/KOKKOS/atom_map_kokkos.cpp
@@ -273,6 +273,7 @@ void AtomKokkos::map_set()
     error->one(FLERR,"Failed to insert into Kokkos hash atom map");
 
   k_sametag.modify_device();
+  k_sametag.sync_host();
 
   if (map_style == MAP_ARRAY)
     k_map_array.modify_device();
-Original file line number
+Diff line change
@@ Expand Up @@
     ----------
-    ..versionadded:: TBD
+    .. versionadded:: TBD
     *Dipoles* section:
@@ Expand Down @@