KOKKOS: port surf collide/react, computes, fix temp/global/rescale, and QK gas reactions

cmake/common/set/sparta_cmake_defaults.cmake

@@ -73,28 +73,6 @@ if(SPARTA_ENABLE_TESTING)
   # the non-KOKKOS configurations.
   if(SPARTA_KOKKOS_EXACT)
     list(APPEND SPARTA_DISABLED_TESTS
-        # fix ave/grid for grid/surf inputs not yet supported in KOKKOS
-        "in.ablation.2d"
-        "in.ablation.3d"
-        # surf_collide adiabatic/cll/td/impulsive styles not KOKKOS-enabled
-        "in.beam.adiabatic"
-        "in.beam.cll"
-        "in.beam.impulsive"
-        "in.beam.td"
-        "in.circle.adiabatic"
-        "in.circle.cll"
-        "in.circle.impulsive"
-        "in.circle.td"
-        # surf_react gs/ps styles use a non-KOKKOS-enabled surf_collide method
-        "in.beam.face.gs"
-        "in.beam.face.gs_ps"
-        "in.beam.face.ps"
-        "in.beam.surf.gs"
-        "in.beam.surf.gs_ps"
-        "in.beam.surf.ps"
-        "in.circle.gs"
-        "in.circle.gs_ps"
-        "in.circle.ps"
         # external field fix not KOKKOS-enabled
         "in.bfield"
         "in.bfield.grid"

doc/Section_commands.html

@@ -346,7 +346,7 @@ <H4>Fix styles
 <TR ALIGN="center"><TD ><A HREF = "fix_ave_surf.html">ave/surf</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance (k)</A></TD><TD ><A HREF = "fix_controller.html">controller</A></TD><TD ><A HREF = "fix_custom.html">custom</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset (k)</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_emit_face.html">emit/face (k)</A></TD><TD ><A HREF = "fix_emit_face_file.html">emit/face/file</A></TD><TD ><A HREF = "fix_emit_surf.html">emit/surf</A></TD><TD ><A HREF = "fix_field_grid.html">field/grid</A></TD><TD ><A HREF = "fix_field_particle.html">field/particle</A></TD><TD ><A HREF = "fix_grid_check.html">grid/check (k)</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_halt.html">halt</A></TD><TD ><A HREF = "fix_move_surf.html">move/surf (k)</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_surf_temp.html">surf/temp</A></TD><TD ><A HREF = "fix_temp_global_rescale.html">temp/global/rescale</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale (k)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_vibmode.html">vibmode (k)</A> 
+<TR ALIGN="center"><TD ><A HREF = "fix_vibmode.html">vibmode (k)</A>
 </TD></TR></TABLE></DIV>
 
 <HR>
@@ -362,9 +362,9 @@ <H4>Compute styles
 </P>
 <DIV ALIGN=center><TABLE  BORDER=1 >
 <TR ALIGN="center"><TD ><A HREF = "compute_boundary.html">boundary (k)</A></TD><TD ><A HREF = "compute_count.html">count (k)</A></TD><TD ><A HREF = "compute_distsurf_grid.html">distsurf/grid (k)</A></TD><TD ><A HREF = "compute_dt_grid.html">dt/grid (k)</A></TD><TD ><A HREF = "compute_eflux_grid.html">eflux/grid (k)</A></TD><TD ><A HREF = "compute_fft_grid.html">fft/grid (k)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_gas_collision_grid.html">gas/collision/grid</A></TD><TD ><A HREF = "compute_gas_collision_tally.html">gas/collision/tally</A></TD><TD ><A HREF = "compute_gas_reaction_grid.html">gas/reaction/grid</A></TD><TD ><A HREF = "compute_gas_reaction_tally.html">gas/reaction/tally</A></TD><TD ><A HREF = "compute_grid.html">grid (k)</A></TD><TD ><A HREF = "compute_isurf_grid.html">isurf/grid</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_ke_particle.html">ke/particle (k)</A></TD><TD ><A HREF = "compute_lambda_grid.html">lambda/grid (k)</A></TD><TD ><A HREF = "compute_pflux_grid.html">pflux/grid (k)</A></TD><TD ><A HREF = "compute_property_grid.html">property/grid (k)</A></TD><TD ><A HREF = "compute_property_surf.html">property/surf</A></TD><TD ><A HREF = "compute_react_boundary.html">react/boundary</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_react_surf.html">react/surf</A></TD><TD ><A HREF = "compute_react_isurf_grid.html">react/isurf/grid</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_sonine_grid.html">sonine/grid (k)</A></TD><TD ><A HREF = "compute_surf.html">surf (k)</A></TD><TD ><A HREF = "compute_surf_collision_tally.html">surf/collision/tally</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_gas_collision_grid.html">gas/collision/grid (k)</A></TD><TD ><A HREF = "compute_gas_collision_tally.html">gas/collision/tally</A></TD><TD ><A HREF = "compute_gas_reaction_grid.html">gas/reaction/grid (k)</A></TD><TD ><A HREF = "compute_gas_reaction_tally.html">gas/reaction/tally</A></TD><TD ><A HREF = "compute_grid.html">grid (k)</A></TD><TD ><A HREF = "compute_isurf_grid.html">isurf/grid (k)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_ke_particle.html">ke/particle (k)</A></TD><TD ><A HREF = "compute_lambda_grid.html">lambda/grid (k)</A></TD><TD ><A HREF = "compute_pflux_grid.html">pflux/grid (k)</A></TD><TD ><A HREF = "compute_property_grid.html">property/grid (k)</A></TD><TD ><A HREF = "compute_property_surf.html">property/surf (k)</A></TD><TD ><A HREF = "compute_react_boundary.html">react/boundary</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_react_surf.html">react/surf (k)</A></TD><TD ><A HREF = "compute_react_isurf_grid.html">react/isurf/grid (k)</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_sonine_grid.html">sonine/grid (k)</A></TD><TD ><A HREF = "compute_surf.html">surf (k)</A></TD><TD ><A HREF = "compute_surf_collision_tally.html">surf/collision/tally</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_surf_reaction_tally.html">surf/reaction/tally</A></TD><TD ><A HREF = "compute_temp.html">temp (k)</A></TD><TD ><A HREF = "compute_thermal_grid.html">thermal/grid (k)</A></TD><TD ><A HREF = "compute_tvib_grid.html">tvib/grid (k)</A> 
 </TD></TR></TABLE></DIV>
 
@@ -393,9 +393,9 @@ <H4>Surface collide styles
 letters in parenthesis: k = KOKKOS.
 </P>
 <DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">adiabatic</A></TD><TD ><A HREF = "surf_collide.html">cll</A></TD><TD ><A HREF = "surf_collide.html">diffuse (k)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">impulsive</A></TD><TD ><A HREF = "surf_collide.html">piston (k)</A></TD><TD ><A HREF = "surf_collide.html">specular (k)</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">td</A></TD><TD ><A HREF = "surf_collide.html">transparent (k)</A></TD><TD ><A HREF = "surf_collide.html">vanish (k)</A> 
+<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">adiabatic (k)</A></TD><TD ><A HREF = "surf_collide.html">cll (k)</A></TD><TD ><A HREF = "surf_collide.html">diffuse (k)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">impulsive (k)</A></TD><TD ><A HREF = "surf_collide.html">piston (k)</A></TD><TD ><A HREF = "surf_collide.html">specular (k)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "surf_collide.html">td (k)</A></TD><TD ><A HREF = "surf_collide.html">transparent (k)</A></TD><TD ><A HREF = "surf_collide.html">vanish (k)</A> 
 </TD></TR></TABLE></DIV>
 
 <HR>
@@ -409,7 +409,7 @@ <H4>Surface reaction styles
 letters in parenthesis: k = KOKKOS.
 </P>
 <DIV ALIGN=center><TABLE  BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "surf_react_adsorb.html">adsorb</A></TD><TD ><A HREF = "surf_react.html">global (k)</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "surf_react_adsorb.html">adsorb (k)</A></TD><TD ><A HREF = "surf_react.html">global (k)</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "surf_react.html">prob (k)</A> 
 </TD></TR></TABLE></DIV>
 

doc/Section_commands.txt

@@ -416,7 +416,7 @@ This is indicated by additional letters in parenthesis: k = KOKKOS.
 "move/surf (k)"_fix_move_surf.html,
 "print"_fix_print.html,
 "surf/temp"_fix_surf_temp.html,
-"temp/global/rescale"_fix_temp_global_rescale.html,
+"temp/global/rescale (k)"_fix_temp_global_rescale.html,
 "temp/rescale (k)"_fix_temp_rescale.html,
 "vibmode (k)"_fix_vibmode.html :tb(c=6,ea=c)
 
@@ -437,20 +437,20 @@ letters in parenthesis: k = KOKKOS.
 "dt/grid (k)"_compute_dt_grid.html,
 "eflux/grid (k)"_compute_eflux_grid.html,
 "fft/grid (k)"_compute_fft_grid.html,
-"gas/collision/grid"_compute_gas_collision_grid.html,
+"gas/collision/grid (k)"_compute_gas_collision_grid.html,
 "gas/collision/tally"_compute_gas_collision_tally.html,
-"gas/reaction/grid"_compute_gas_reaction_grid.html,
+"gas/reaction/grid (k)"_compute_gas_reaction_grid.html,
 "gas/reaction/tally"_compute_gas_reaction_tally.html,
 "grid (k)"_compute_grid.html,
-"isurf/grid"_compute_isurf_grid.html,
+"isurf/grid (k)"_compute_isurf_grid.html,
 "ke/particle (k)"_compute_ke_particle.html,
 "lambda/grid (k)"_compute_lambda_grid.html,
 "pflux/grid (k)"_compute_pflux_grid.html,
 "property/grid (k)"_compute_property_grid.html,
-"property/surf"_compute_property_surf.html,
+"property/surf (k)"_compute_property_surf.html,
 "react/boundary"_compute_react_boundary.html,
-"react/surf"_compute_react_surf.html,
-"react/isurf/grid"_compute_react_isurf_grid.html,
+"react/surf (k)"_compute_react_surf.html,
+"react/isurf/grid (k)"_compute_react_isurf_grid.html,
 "reduce"_compute_reduce.html,
 "sonine/grid (k)"_compute_sonine_grid.html,
 "surf (k)"_compute_surf.html,
@@ -482,13 +482,13 @@ used if SPARTA is built with the "appropriate accelerated
 package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: k = KOKKOS.
 
-"adiabatic"_surf_collide.html,
-"cll"_surf_collide.html,
+"adiabatic (k)"_surf_collide.html,
+"cll (k)"_surf_collide.html,
 "diffuse (k)"_surf_collide.html,
-"impulsive"_surf_collide.html,
+"impulsive (k)"_surf_collide.html,
 "piston (k)"_surf_collide.html,
 "specular (k)"_surf_collide.html,
-"td"_surf_collide.html,
+"td (k)"_surf_collide.html,
 "transparent (k)"_surf_collide.html,
 "vanish (k)"_surf_collide.html :tb(c=3,ea=c)
 
@@ -502,6 +502,6 @@ used if SPARTA is built with the "appropriate accelerated
 package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: k = KOKKOS.
 
-"adsorb"_surf_react_adsorb.html,
+"adsorb (k)"_surf_react_adsorb.html,
 "global (k)"_surf_react.html,
 "prob (k)"_surf_react.html :tb(c=2,ea=c)

doc/compute_isurf_grid.html

@@ -11,6 +11,8 @@
 
 <H3>compute isurf/grid command 
 </H3>
+<H3>compute isurf/grid/kk command 
+</H3>
 <P><B>Syntax:</B>
 </P>
 <PRE>compute ID isurf/grid group-ID mix-ID value1 value2 ... 
@@ -159,6 +161,29 @@ <H3>compute isurf/grid command
 </P>
 <HR>
 
+<P>Styles with a <I>kk</I> suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+<A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+</P>
+<P>These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
+SPARTA</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke SPARTA, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See the <A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/compute_isurf_grid.txt

@@ -7,6 +7,7 @@
 :line
 
 compute isurf/grid command :h3
+compute isurf/grid/kk command :h3
 
 [Syntax:]
 
@@ -149,6 +150,29 @@ for 2d simulations.
 
 :line
 
+Styles with a {kk} suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+"Accelerating SPARTA"_Section_accelerate.html section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+
+These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the "Making
+SPARTA"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke SPARTA, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See the "Accelerating SPARTA"_Section_accelerate.html section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+
+:line
+
 [Restrictions:] none
 
 [Related commands:]

doc/compute_property_surf.html

@@ -11,6 +11,8 @@
 
 <H3>compute property/surf command 
 </H3>
+<H3>compute property/surf/kk command 
+</H3>
 <P><B>Syntax:</B>
 </P>
 <PRE>compute ID property/surf group-ID input1 input2 ... 
@@ -109,6 +111,29 @@ <H3>compute property/surf command
 </P>
 <HR>
 
+<P>Styles with a <I>kk</I> suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+<A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+</P>
+<P>These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
+SPARTA</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke SPARTA, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See the <A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+</P>
+<HR>
+
 <P><B>Restrictions:</B>
 </P>
 <P>For 2d simulations, none of the attributes which refer to the 3rd

doc/compute_property_surf.txt

@@ -7,6 +7,7 @@
 :line
 
 compute property/surf command :h3
+compute property/surf/kk command :h3
 
 [Syntax:]
 
@@ -101,6 +102,29 @@ length units for {area} in 2d, area units for {area} in 3d.
 
 :line
 
+Styles with a {kk} suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+"Accelerating SPARTA"_Section_accelerate.html section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+
+These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the "Making
+SPARTA"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke SPARTA, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See the "Accelerating SPARTA"_Section_accelerate.html section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+
+:line
+
 [Restrictions:]
 
 For 2d simulations, none of the attributes which refer to the 3rd

doc/compute_react_isurf_grid.html

@@ -11,6 +11,8 @@
 
 <H3>compute react/isurf/grid command 
 </H3>
+<H3>compute react/isurf/grid/kk command 
+</H3>
 <P><B>Syntax:</B>
 </P>
 <PRE>compute ID react/isurf/grid group-ID reaction-ID value1 value2 ... 
@@ -116,6 +118,29 @@ <H3>compute react/isurf/grid command
 </P>
 <HR>
 
+<P>Styles with a <I>kk</I> suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+<A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+</P>
+<P>These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
+SPARTA</A> section for more info.
+</P>
+<P>You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
+switch</A> when you invoke SPARTA, or you can
+use the <A HREF = "suffix.html">suffix</A> command in your input script.
+</P>
+<P>See the <A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+</P>
+<HR>
+
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/compute_react_isurf_grid.txt

@@ -7,6 +7,7 @@
 :line
 
 compute react/isurf/grid command :h3
+compute react/isurf/grid/kk command :h3
 
 [Syntax:]
 
@@ -106,6 +107,29 @@ occurred on surface elements in that grid cell.
 
 :line
 
+Styles with a {kk} suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in the
+"Accelerating SPARTA"_Section_accelerate.html section of the manual.
+The accelerated styles take the same arguments and should produce the
+same results, except for different random number, round-off and
+precision issues.
+
+These accelerated styles are part of the KOKKOS package. They are only
+enabled if SPARTA was built with that package.  See the "Making
+SPARTA"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke SPARTA, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See the "Accelerating SPARTA"_Section_accelerate.html section of the
+manual for more instructions on how to use the accelerated styles
+effectively.
+
+:line
+
 [Restrictions:] none
 
 [Related commands:]