diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 0e44f150f7..a72dd139e8 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1486,12 +1486,6 @@ info, etc) and stores the values in a local vector or array. These are produced as output values which can be used as input to other output commands.

-

The compute atom/molecule command takes a -list of one or more per-atom quantities (from a compute, fix, per-atom -variable) and sums the quantities on a per-molecule basis. It -produces a global vector or array as output values which can be used -as input to other output commands. -

Fixes that process output quantities

The fix vector command can create global vectors as @@ -1573,7 +1567,6 @@ vector input could be a column of an array. compute slice global vectors/arrays global vector/array compute property/atom per-atom vectors per-atom vector/array compute property/local local vectors local vector/array -compute atom/molecule per-atom vectors global vector/array fix vector global scalars global vector fix ave/atom per-atom vectors per-atom vector/array fix ave/time global scalars/vectors global scalar/vector/array, file diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index bccfea1882..d65f405e7a 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1475,12 +1475,6 @@ info, etc) and stores the values in a local vector or array. These are produced as output values which can be used as input to other output commands. -The "compute atom/molecule"_compute_atom_molecule.html command takes a -list of one or more per-atom quantities (from a compute, fix, per-atom -variable) and sums the quantities on a per-molecule basis. It -produces a global vector or array as output values which can be used -as input to other output commands. - Fixes that process output quantities :h5,link(fixoutput) The "fix vector"_fix_vector.html command can create global vectors as @@ -1561,7 +1555,6 @@ Command: Input: Output: "compute slice"_compute_slice.html: global vectors/arrays: global vector/array: "compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: "compute property/local"_compute_property_local.html: local vectors: local vector/array: -"compute atom/molecule"_compute_atom_molecule.html: per-atom vectors: global vector/array: "fix vector"_fix_vector.html: global scalars: global vector: "fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: "fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: diff --git a/doc/compute_angmom_chunk.html b/doc/compute_angmom_chunk.html index 24ee7fdc55..2017422f12 100644 --- a/doc/compute_angmom_chunk.html +++ b/doc/compute_angmom_chunk.html @@ -16,7 +16,7 @@ 

compute ID group-ID angmom/chunk chunkID

Examples: diff --git a/doc/compute_angmom_chunk.txt b/doc/compute_angmom_chunk.txt index 26fe5a5ec6..90dc095d92 100644 --- a/doc/compute_angmom_chunk.txt +++ b/doc/compute_angmom_chunk.txt @@ -13,7 +13,7 @@ compute angmom/chunk command :h3 compute ID group-ID angmom/chunk chunkID :pre ID, group-ID are documented in "compute"_compute.html command -angmom/molecule = style name of this compute command +angmom/chunk = style name of this compute command chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul [Examples:] diff --git a/doc/compute_com.html b/doc/compute_com.html index c9a4441cec..64735c5cf5 100644 --- a/doc/compute_com.html +++ b/doc/compute_com.html @@ -55,7 +55,7 @@ distance units.

Related commands:

-

compute com/molecule +

compute com/chunk

Default: none

diff --git a/doc/compute_com.txt b/doc/compute_com.txt index 9198a8f10f..cb6aa830e4 100644 --- a/doc/compute_com.txt +++ b/doc/compute_com.txt @@ -52,6 +52,6 @@ distance "units"_units.html. [Related commands:] -"compute com/molecule"_compute_com_molecule.html +"compute com/chunk"_compute_com_chunk.html [Default:] none diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index e5633840da..8d0eed96f2 100644 --- a/doc/compute_gyration.html +++ b/doc/compute_gyration.html @@ -71,7 +71,7 @@ distance^2 units respectively.

Related commands:

-

compute gyration/molecule +

compute gyration/chunk

Default: none

diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index 7eb56a1584..84d6e64a23 100644 --- a/doc/compute_gyration.txt +++ b/doc/compute_gyration.txt @@ -68,6 +68,6 @@ distance^2 "units"_units.html respectively. [Related commands:] -"compute gyration/molecule"_compute_gyration_molecule.html +"compute gyration/chunk"_compute_gyration_chunk.html [Default:] none diff --git a/doc/compute_inertia_chunk.html b/doc/compute_inertia_chunk.html index 3dfb2e5e69..9b131c32a0 100644 --- a/doc/compute_inertia_chunk.html +++ b/doc/compute_inertia_chunk.html @@ -16,7 +16,7 @@ 
compute ID group-ID inertia/chunk chunkID

Examples: diff --git a/doc/compute_inertia_chunk.txt b/doc/compute_inertia_chunk.txt index 5d482a5333..b3bed44b43 100644 --- a/doc/compute_inertia_chunk.txt +++ b/doc/compute_inertia_chunk.txt @@ -13,7 +13,7 @@ compute inertia/chunk command :h3 compute ID group-ID inertia/chunk chunkID :pre ID, group-ID are documented in "compute"_compute.html command -inertia/molecule = style name of this compute command +inertia/chunk = style name of this compute command chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul [Examples:] diff --git a/doc/compute_msd.html b/doc/compute_msd.html index a621b16d12..137e89cb60 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -89,8 +89,8 @@ distance^2 units.

compute msd/nongauss, compute displace_atom, fix -store/state, compute -msd/molecule +store/state, compute +msd/chunk

Default:

diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt index c2e93d4ea8..9ada35314c 100644 --- a/doc/compute_msd.txt +++ b/doc/compute_msd.txt @@ -82,7 +82,7 @@ distance^2 "units"_units.html. "compute msd/nongauss"_compute_msd_nongauss.html, "compute displace_atom"_compute_displace_atom.html, "fix store/state"_fix_store_state.html, "compute -msd/molecule"_compute_msd_molecule.html +msd/chunk"_compute_msd_chunk.html [Default:] diff --git a/doc/compute_msd_chunk.html b/doc/compute_msd_chunk.html index f0a5016b03..e6ef5bc252 100644 --- a/doc/compute_msd_chunk.html +++ b/doc/compute_msd_chunk.html @@ -16,7 +16,7 @@ 
compute ID group-ID msd/chunk chunkID

Examples: diff --git a/doc/compute_msd_chunk.txt b/doc/compute_msd_chunk.txt index 45427ee7a2..98dc5ed937 100644 --- a/doc/compute_msd_chunk.txt +++ b/doc/compute_msd_chunk.txt @@ -13,7 +13,7 @@ compute msd/chunk command :h3 compute ID group-ID msd/chunk chunkID :pre ID, group-ID are documented in "compute"_compute.html command -msd/molecule = style name of this compute command +msd/chunk = style name of this compute command chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul [Examples:] diff --git a/doc/compute_omega_chunk.html b/doc/compute_omega_chunk.html index b91a512b59..3c553afbc8 100644 --- a/doc/compute_omega_chunk.html +++ b/doc/compute_omega_chunk.html @@ -16,7 +16,7 @@ 

compute ID group-ID omega/chunk chunkID

Examples: diff --git a/doc/compute_omega_chunk.txt b/doc/compute_omega_chunk.txt index b829bc6cdb..2db841bad8 100644 --- a/doc/compute_omega_chunk.txt +++ b/doc/compute_omega_chunk.txt @@ -13,7 +13,7 @@ compute omega/chunk command :h3 compute ID group-ID omega/chunk chunkID :pre ID, group-ID are documented in "compute"_compute.html command -omega/molecule = style name of this compute command +omega/chunk = style name of this compute command chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul [Examples:] diff --git a/doc/compute_torque_chunk.html b/doc/compute_torque_chunk.html index 495cad9526..593397646d 100644 --- a/doc/compute_torque_chunk.html +++ b/doc/compute_torque_chunk.html @@ -16,7 +16,7 @@ 

compute ID group-ID torque/chunk chunkID

Examples: diff --git a/doc/compute_torque_chunk.txt b/doc/compute_torque_chunk.txt index ddd6914e06..df27c39a9e 100644 --- a/doc/compute_torque_chunk.txt +++ b/doc/compute_torque_chunk.txt @@ -13,7 +13,7 @@ compute torque/chunk command :h3 compute ID group-ID torque/chunk chunkID :pre ID, group-ID are documented in "compute"_compute.html command -torque/molecule = style name of this compute command +torque/chunk = style name of this compute command chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul [Examples:] diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html index 64a299a4e5..b4d3879253 100644 --- a/doc/fix_ave_histo.html +++ b/doc/fix_ave_histo.html @@ -109,11 +109,11 @@ arrays), depending on the setting of the mode keyword.

If mode = vector, then the input values may either be vectors or arrays. If a global array is listed, then it is the same as if the individual columns of the array had been listed one by one. -E.g. these 2 fix ave/histo commands are equivalent, since the compute -com/molecule command creates a global array +E.g. these 2 fix ave/histo commands are equivalent, since the compute +com/chunk command creates a global array with 3 columns:

-
compute myCOM all com/molecule
+
compute myCOM all com/chunk
 fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
 fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector 
 

diff --git a/doc/fix_ave_histo.txt b/doc/fix_ave_histo.txt
index 1d7a1d6163..62e7c837b4 100644
--- a/doc/fix_ave_histo.txt
+++ b/doc/fix_ave_histo.txt
@@ -95,10 +95,10 @@ If {mode} = vector, then the input values may either be vectors or
 arrays.  If a global array is listed, then it is the same as if the
 individual columns of the array had been listed one by one.
 E.g. these 2 fix ave/histo commands are equivalent, since the "compute
-com/molecule"_compute_com_molecule.html command creates a global array
+com/chunk"_compute_com_chunk.html command creates a global array
 with 3 columns:
 
-compute myCOM all com/molecule
+compute myCOM all com/chunk
 fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector
 fix 2 all ave/histo 100 1 100 c_myCOM\[1\] c_myCOM\[2\] c_myCOM\[3\] file tmp2.com mode vector :pre