From ccefc1c3c0e7a27e8146bb4c4f6da3229dc3f451 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 4 Dec 2009 21:04:00 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3509 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_howto.html | 14 ++++++------- doc/Section_howto.txt | 14 ++++++------- doc/compute.html | 10 ++++----- doc/compute.txt | 10 ++++----- doc/compute_centro_atom.html | 8 ++++---- doc/compute_centro_atom.txt | 8 ++++---- doc/compute_cna_atom.html | 8 ++++---- doc/compute_cna_atom.txt | 8 ++++---- doc/compute_coord_atom.html | 8 ++++---- doc/compute_coord_atom.txt | 8 ++++---- doc/compute_damage_atom.html | 8 ++++---- doc/compute_damage_atom.txt | 8 ++++---- doc/compute_displace_atom.html | 8 ++++---- doc/compute_displace_atom.txt | 8 ++++---- doc/compute_ke_atom.html | 8 ++++---- doc/compute_ke_atom.txt | 8 ++++---- doc/compute_pe_atom.html | 8 ++++---- doc/compute_pe_atom.txt | 8 ++++---- doc/compute_reduce.html | 10 ++++----- doc/compute_reduce.txt | 10 ++++----- doc/compute_stress_atom.html | 8 ++++---- doc/compute_stress_atom.txt | 8 ++++---- doc/dump.html | 18 ++++++++--------- doc/dump.txt | 18 ++++++++--------- doc/fix.html | 2 +- doc/fix.txt | 2 +- doc/fix_ave_atom.html | 36 ++++++++++++++++----------------- doc/fix_ave_atom.txt | 36 ++++++++++++++++----------------- doc/fix_ave_spatial.html | 30 +++++++++++++-------------- doc/fix_ave_spatial.txt | 30 +++++++++++++-------------- doc/fix_coord_original.html | 6 +++--- doc/fix_coord_original.txt | 6 +++--- doc/fix_move.html | 6 +++--- doc/fix_move.txt | 6 +++--- doc/variable.html | 4 ++-- doc/variable.txt | 4 ++-- lib/atc/ATC_Transfer.cpp | 2 +- lib/atc/ATC_Transfer.h | 4 ++-- lib/atc/ATC_TransferThermal.cpp | 2 +- lib/atc/LammpsInterface.cpp | 8 ++++---- 40 files changed, 208 insertions(+), 208 deletions(-) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 4cd1fe78ef..b809af9fa0 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1136,18 +1136,18 @@ frequencies and global vs per-atom attributes are the same.
- + - + - - + + - - + + - +
Command Input Input Freq Output Output Freq
thermo_style custom thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable nthermo screen, log nthermo
dump custom keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable dump freq file dump freq
dump custom keyword, per-atom compute, per-atom fix, atom variable dump freq file dump freq
global fixes N/A N/A global scalar/vector 1 or nevery
peratom fixes N/A N/A peratom scalar/vector 1 or nevery
per-atom fixes N/A N/A per-atom vector/array 1 or nevery
fix ave/time global scalar/vector fix, global scalar/vector compute, equal variable nevery global scalar/vector, file nfreq
fix ave/spatial peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number nevery global vector nfreq, file
fix ave/atom peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector nevery peratom scalar/vector nfreq
fix ave/spatial per-atom fix, per-atom compute, atom vector, atom variable, density mass/number nevery global vector nfreq, file
fix ave/atom per-atom compute, per-atom fix, atom variable, atom vector nevery per-atom vector/array nfreq
fix print any variable nevery screen, file nevery
global computes N/A N/A global scalar/vector N/A
peratom computes N/A N/A peratom scalar/vector N/A
compute sum peratom scalar/vector compute, peratom scalar/vector fix, atom variable N/A global scalar/vector N/A
per-atom computes N/A N/A per-atom vector/array N/A
compute sum per-atom compute, per-atom fix, atom variable N/A global scalar/vector N/A
variable equal thermo keywords, atom value vx[123], global scalar/vector compute, global scalar/vector fix, non-atom variable N/A global scalar N/A
variable atom thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable N/A peratom scalar N/A
variable atom thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, per-atom compute, global fix, per-atom fix, any variable N/A per-atom vector N/A
print any variable N/A screen, log between runs
run every any variable nevery screen, log nevery
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 4c57cdddac..34b513d11f 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1128,18 +1128,18 @@ frequencies and global vs per-atom attributes are the same. Command: Input: Input Freq: Output: Output Freq thermo_style custom: thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable: nthermo: screen, log: nthermo -dump custom: keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable: dump freq: file: dump freq +dump custom: keyword, per-atom compute, per-atom fix, atom variable: dump freq: file: dump freq global fixes: N/A: N/A: global scalar/vector: 1 or nevery -peratom fixes: N/A: N/A: peratom scalar/vector: 1 or nevery +per-atom fixes: N/A: N/A: per-atom vector/array: 1 or nevery fix ave/time: global scalar/vector fix, global scalar/vector compute, equal variable: nevery: global scalar/vector, file: nfreq -fix ave/spatial: peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file -fix ave/atom: peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector: nevery: peratom scalar/vector: nfreq +fix ave/spatial: per-atom fix, per-atom compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file +fix ave/atom: per-atom compute, per-atom fix, atom variable, atom vector: nevery: per-atom vector/array: nfreq fix print: any variable: nevery: screen, file: nevery global computes: N/A: N/A: global scalar/vector: N/A -peratom computes: N/A: N/A: peratom scalar/vector: N/A -compute sum: peratom scalar/vector compute, peratom scalar/vector fix, atom variable: N/A: global scalar/vector: N/A +per-atom computes: N/A: N/A: per-atom vector/array: N/A +compute sum: per-atom compute, per-atom fix, atom variable: N/A: global scalar/vector: N/A variable equal: thermo keywords, atom value vx\[123\], global scalar/vector compute, global scalar/vector fix, non-atom variable: N/A: global scalar: N/A -variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable: N/A: peratom scalar: N/A +variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, per-atom compute, global fix, per-atom fix, any variable: N/A: per-atom vector: N/A print: any variable: N/A: screen, log: between runs run every: any variable: nevery: screen, log: nevery :tb(s=:) diff --git a/doc/compute.html b/doc/compute.html index e245983a02..beca436ef9 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -46,11 +46,11 @@ calculate a global temperature or pressure can be used by fixes that do thermostatting or barostatting and when atom velocities are created.

-

The results of per-atom computes can be output via the dump -custom command or the fix -ave/spatial command. Or the per-atom values can -be time-averaged via the fix ave/atom command and -then output via the dump custom or fix +

The results of per-atom computes that calculate a per-atom vector or +array can be output via the dump custom command or the +fix ave/spatial command. Or the per-atom +values can be time-averaged via the fix ave/atom +command and then output via the dump custom or fix ave/spatial commands. Or the per-atom values can be referenced in a variable atom command. Note that the value of per-atom computes will be 0.0 for atoms not in the diff --git a/doc/compute.txt b/doc/compute.txt index e8a5cc8ed4..b834ccfba6 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -43,11 +43,11 @@ calculate a global temperature or pressure can be used by fixes that do thermostatting or barostatting and when atom velocities are created. -The results of per-atom computes can be output via the "dump -custom"_dump.html command or the "fix -ave/spatial"_fix_ave_spatial.html command. Or the per-atom values can -be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and -then output via the "dump custom"_dump.html or "fix +The results of per-atom computes that calculate a per-atom vector or +array can be output via the "dump custom"_dump.html command or the +"fix ave/spatial"_fix_ave_spatial.html command. Or the per-atom +values can be time-averaged via the "fix ave/atom"_fix_ave_atom.html +command and then output via the "dump custom"_dump.html or "fix ave/spatial"_fix_ave_spatial.html commands. Or the per-atom values can be referenced in a "variable atom"_variable.html command. Note that the value of per-atom computes will be 0.0 for atoms not in the diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html index de92e1a273..b33d73c532 100644 --- a/doc/compute_centro_atom.html +++ b/doc/compute_centro_atom.html @@ -52,10 +52,10 @@ too frequently or to have multiple compute/dump commands, each with a

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions: none

diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt index 6d935246d7..e2d12163aa 100644 --- a/doc/compute_centro_atom.txt +++ b/doc/compute_centro_atom.txt @@ -49,10 +49,10 @@ too frequently or to have multiple compute/dump commands, each with a [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] none diff --git a/doc/compute_cna_atom.html b/doc/compute_cna_atom.html index f581e28b28..c6bebc7d5b 100644 --- a/doc/compute_cna_atom.html +++ b/doc/compute_cna_atom.html @@ -75,10 +75,10 @@ too frequently or to have multiple compute/dump commands, each with a

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions: none

diff --git a/doc/compute_cna_atom.txt b/doc/compute_cna_atom.txt index d67778dbe4..d27c971603 100644 --- a/doc/compute_cna_atom.txt +++ b/doc/compute_cna_atom.txt @@ -72,10 +72,10 @@ too frequently or to have multiple compute/dump commands, each with a [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] none diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index beabf3d1f8..adc0badd3b 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -44,10 +44,10 @@ too frequently or to have multiple compute/dump commands, each of a

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions: none

diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index f8c888b2bc..4e9797f4b4 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -41,10 +41,10 @@ too frequently or to have multiple compute/dump commands, each of a [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] none diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html index d060006f33..70130810b4 100644 --- a/doc/compute_damage_atom.html +++ b/doc/compute_damage_atom.html @@ -35,10 +35,10 @@ compute group.

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions:

diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt index 57421804c1..a1796f59d8 100644 --- a/doc/compute_damage_atom.txt +++ b/doc/compute_damage_atom.txt @@ -32,10 +32,10 @@ compute group. [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index c5db4ae1bf..c3998f89f5 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -74,10 +74,10 @@ file.

Output info:

-

This compute calculates a vector of length 4 for each atom, which can -be accessed by indices 1-4 by any command that uses per-atom values -from a compute as input. See this section -for an overview of LAMMPS output options. +

This compute calculates a per-atom array with 4 columns, which can be +accessed by indices 1-4 by any command that uses per-atom values from +a compute as input. See this section for an +overview of LAMMPS output options.

Restrictions: none

diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index 94df70a5c3..39a11639ad 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -71,10 +71,10 @@ file. [Output info:] -This compute calculates a vector of length 4 for each atom, which can -be accessed by indices 1-4 by any command that uses per-atom values -from a compute as input. See "this section"_Section_howto.html#4_15 -for an overview of LAMMPS output options. +This compute calculates a per-atom array with 4 columns, which can be +accessed by indices 1-4 by any command that uses per-atom values from +a compute as input. See "this section"_Section_howto.html#4_15 for an +overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html index f636c1e138..c0a6da8234 100644 --- a/doc/compute_ke_atom.html +++ b/doc/compute_ke_atom.html @@ -35,10 +35,10 @@ specified compute group.

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions: none

diff --git a/doc/compute_ke_atom.txt b/doc/compute_ke_atom.txt index 4cb0036c4c..22c1879a70 100644 --- a/doc/compute_ke_atom.txt +++ b/doc/compute_ke_atom.txt @@ -32,10 +32,10 @@ specified compute group. [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] none diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index ce2dffc64e..edb96f33e4 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -65,10 +65,10 @@ contribution can easily be computed.

Output info:

-

This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See this section for an overview of -LAMMPS output options. +

This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +this section for an overview of LAMMPS +output options.

Restrictions:

diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index 3decb01487..505962e0ee 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -62,10 +62,10 @@ contribution can easily be computed. [Output info:] -This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom values from a compute as -input. See "this section"_Section_howto.html#4_15 for an overview of -LAMMPS output options. +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. [Restrictions:] diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html index f00f209499..6970993bca 100644 --- a/doc/compute_reduce.html +++ b/doc/compute_reduce.html @@ -32,11 +32,11 @@
  • input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name 
      x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  c_ID = per-atom vector value calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
+  f_ID = per-atom vector value calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
+  v_name = per-atom vector calculated by an atom-style variable with name
    diff --git a/doc/compute_reduce.txt b/doc/compute_reduce.txt index 4e2a7090ef..e7e208653b 100644 --- a/doc/compute_reduce.txt +++ b/doc/compute_reduce.txt @@ -22,11 +22,11 @@ mode = {sum} or {min} or {max} :l one or more inputs can be listed :l input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) - c_ID = per-atom scalar value calculated by a compute with ID - c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID - f_ID = per-atom scalar value calculated by a fix with ID - f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID - v_name = per-atom value calculated by an atom-style variable with name :pre + c_ID = per-atom vector value calculated by a compute with ID + c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector value calculated by a fix with ID + f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name :pre :ule [Examples:] diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index 92d04fa2fd..300e21d796 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -100,10 +100,10 @@ contribution can easily be computed.

    Output info:

    -

    This compute calculates a vector of length 6 for each atom, which can -be accessed by indices 1-6 by any command that uses per-atom values -from a compute as input. See this section -for an overview of LAMMPS output options. +

    This compute calculates a per-atom array with 6 columns, which can be +accessed by indices 1-6 by any command that uses per-atom values from +a compute as input. See this section for an +overview of LAMMPS output options.

    Restrictions: none

    diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index 7e6dfbe2a4..848b397e2f 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -97,10 +97,10 @@ contribution can easily be computed. [Output info:] -This compute calculates a vector of length 6 for each atom, which can -be accessed by indices 1-6 by any command that uses per-atom values -from a compute as input. See "this section"_Section_howto.html#4_15 -for an overview of LAMMPS output options. +This compute calculates a per-atom array with 6 columns, which can be +accessed by indices 1-6 by any command that uses per-atom values from +a compute as input. See "this section"_Section_howto.html#4_15 for an +overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/dump.html b/doc/dump.html index 8904d25ea0..625d2f4296 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -58,11 +58,11 @@ angmomx,angmomy,angmomz = angular momentum of extended particle quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles - c_ID = per-atom scalar value calculated by a compute with ID - c_ID[N] = Nth component of per-atom vector calculated by a compute with ID - f_ID = per-atom scalar value calculated by a fix with ID - f_ID[N] = Nth component of per-atom vector calculated by a fix with ID - v_name = per-atom value calculated by an atom-style variable with name + c_ID = per-atom vector value calculated by a compute with ID + c_ID[N] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector value calculated by a fix with ID + f_ID[N] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name @@ -331,8 +331,8 @@ custom command.

    If c_ID is used as a keyword, then the scalar per-atom quantity calculated by the compute is printed. If c_ID[N] is used, then N -must be in the range from 1-M, which will print the Nth component of -the M-length per-atom vector calculated by the compute. +must be in the range from 1-M, which will print the Nth column of +the M-length per-atom array calculated by the compute.

    The f_ID and f_ID[N] keywords allow scalar or vector per-atom quantities calculated by a fix to be output. The ID in the @@ -346,8 +346,8 @@ be written to a dump file.

    If f_ID is used as a keyword, then the scalar per-atom quantity calculated by the fix is printed. If f_ID[N] is used, then N must -be in the range from 1-M, which will print the Nth component of the -M-length per-atom vector calculated by the fix. +be in the range from 1-M, which will print the Nth column of the +M-length per-atom array calculated by the fix.

    The v_name keyword allows per-atom quantities calculated by a variable to be output. The name in the keyword should diff --git a/doc/dump.txt b/doc/dump.txt index e15595135c..e4eaf27904 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -49,11 +49,11 @@ args = list of arguments for a particular style :l angmomx,angmomy,angmomz = angular momentum of extended particle quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles - c_ID = per-atom scalar value calculated by a compute with ID - c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID - f_ID = per-atom scalar value calculated by a fix with ID - f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID - v_name = per-atom value calculated by an atom-style variable with name :pre + c_ID = per-atom vector value calculated by a compute with ID + c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector value calculated by a fix with ID + f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name :pre :ule [Examples:] @@ -321,8 +321,8 @@ custom"_thermo_style.html command. If {c_ID} is used as a keyword, then the scalar per-atom quantity calculated by the compute is printed. If {c_ID\[N\]} is used, then N -must be in the range from 1-M, which will print the Nth component of -the M-length per-atom vector calculated by the compute. +must be in the range from 1-M, which will print the Nth column of +the M-length per-atom array calculated by the compute. The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom quantities calculated by a "fix"_fix.html to be output. The ID in the @@ -336,8 +336,8 @@ be written to a dump file. If {f_ID} is used as a keyword, then the scalar per-atom quantity calculated by the fix is printed. If {f_ID\[N\]} is used, then N must -be in the range from 1-M, which will print the Nth component of the -M-length per-atom vector calculated by the fix. +be in the range from 1-M, which will print the Nth column of the +M-length per-atom array calculated by the fix. The {v_name} keyword allows per-atom quantities calculated by a "variable"_variable.html to be output. The name in the keyword should diff --git a/doc/fix.html b/doc/fix.html index 79e34a3f9f..57f5b0753e 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -71,7 +71,7 @@ accessed by various commands for output, including equ atom-style variables, thermo_style custom, and fix ave/time.

    -

    Some fixes calculate a per-atom scalar or vector quantity which can be +

    Some fixes calculate a per-atom vector or array quantity which can be accessed by various commands for output, including atom-style variables, dump_style custom, and fix ave/spatial. diff --git a/doc/fix.txt b/doc/fix.txt index 0c089348f8..fb9cf4722e 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -68,7 +68,7 @@ accessed by various commands for output, including "equal- and atom-style variables"_variable.html, "thermo_style custom"_thermo_style.html, and "fix ave/time"_fix_ave_time.html. -Some fixes calculate a per-atom scalar or vector quantity which can be +Some fixes calculate a per-atom vector or array quantity which can be accessed by various commands for output, including "atom-style variables"_variable.html, "dump_style custom"_dump.html, and "fix ave/spatial"_fix_ave_spatial.html. diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html index 7fdcd96c2a..a0c232f1b6 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -30,11 +30,11 @@

  • value = x, y, z, xu, yu, zu, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name 
      x,y,z,xu,yu,zu,vx,vy,vz,fx,fy,fz = atom attribute (position, unwrapped position, velocity, force component)
-  c_ID = per-atom scalar value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  c_ID = per-atom vector value calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
+  f_ID = per-atom vector value calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
+  v_name = per-atom vector calculated by an atom-style variable with name
    @@ -101,19 +101,19 @@ is meant by image flags.

    If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the compute is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the compute is used. Users can also write code for their own -compute styles and add them to LAMMPS. +appended, the per-atom vector calculated by the compute is used. If a +bracketed term is appended, the Nth columnd of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and add them to LAMMPS.

    If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the fix is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the fix is used. Note that some fixes only produce their values on -certain timesteps, which must be compatible with Nevery, else an -error will results. Users can also write code for their own fix -styles and add them to LAMMPS. +appended, the per-atom vector calculated by the fix is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +Nevery, else an error will results. Users can also write code for +their own fix styles and add them to LAMMPS.

    If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Variables of style @@ -131,10 +131,10 @@ are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various output commands.

    -

    This fix produces a per-atom scalar or vector which can be accessed by -various output commands. A scalar is +

    This fix produces a per-atom vector or array which can be accessed by +various output commands. A vector is produced if only a single quantity is averaged by this fix. If two or -more quantities are averaged, then a vector of values is produced. +more quantities are averaged, then an array of values is produced. The per-atom values can only be accessed on timesteps that are multiples of Nfreq since that is when averaging is performed.

    diff --git a/doc/fix_ave_atom.txt b/doc/fix_ave_atom.txt index 77b22fa2d1..309efb6d2e 100644 --- a/doc/fix_ave_atom.txt +++ b/doc/fix_ave_atom.txt @@ -20,11 +20,11 @@ Nfreq = timestep frequency at which the average value is calculated :l one or more values can be listed :l value = x, y, z, xu, yu, zu, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l x,y,z,xu,yu,zu,vx,vy,vz,fx,fy,fz = atom attribute (position, unwrapped position, velocity, force component) - c_ID = per-atom scalar value calculated by a compute with ID - c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID - f_ID = per-atom scalar value calculated by a fix with ID - f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID - v_name = per-atom value calculated by an atom-style variable with name :pre + c_ID = per-atom vector value calculated by a compute with ID + c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector value calculated by a fix with ID + f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name :pre :ule [Examples:] @@ -90,19 +90,19 @@ is meant by image flags. If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the compute is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. +appended, the per-atom vector calculated by the compute is used. If a +bracketed term is appended, the Nth columnd of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the fix is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the fix is used. Note that some fixes only produce their values on -certain timesteps, which must be compatible with {Nevery}, else an -error will results. Users can also write code for their own fix -styles and "add them to LAMMPS"_Section_modify.html. +appended, the per-atom vector calculated by the fix is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +{Nevery}, else an error will results. Users can also write code for +their own fix styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Variables of style @@ -120,10 +120,10 @@ are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various "output commands"_Section_howto.html#4_15. -This fix produces a per-atom scalar or vector which can be accessed by -various "output commands"_Section_howto.html#4_15. A scalar is +This fix produces a per-atom vector or array which can be accessed by +various "output commands"_Section_howto.html#4_15. A vector is produced if only a single quantity is averaged by this fix. If two or -more quantities are averaged, then a vector of values is produced. +more quantities are averaged, then an array of values is produced. The per-atom values can only be accessed on timesteps that are multiples of {Nfreq} since that is when averaging is performed. diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index 26e1e2d0ad..406ad0b3f6 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -37,11 +37,11 @@ 
      x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
   density/number, density/mass = number or mass density
-  c_ID = per-atom scalar value calculated by a compute with ID
-  c_ID[N] = Nth component of per-atom vector calculated by a compute with ID
-  f_ID = per-atom scalar value calculated by a fix with ID
-  f_ID[N] = Nth component of per-atom vector calculated by a fix with ID
-  v_name = per-atom value calculated by an atom-style variable with name 
+  c_ID = per-atom vector value calculated by a compute with ID
+  c_ID[N] = Nth column of per-atom array calculated by a compute with ID
+  f_ID = per-atom vector value calculated by a fix with ID
+  f_ID[N] = Nth column of per-atom array calculated by a fix with ID
+  v_name = per-atom vector calculated by an atom-style variable with name
  • zero or more keyword/arg pairs may be appended @@ -156,19 +156,19 @@ output.

    If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the compute is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the compute is used. Users can also write code for their own -compute styles and add them to LAMMPS. +appended, the per-atom vector calculated by the compute is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and add them to LAMMPS.

    If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the fix is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the fix is used. Note that some fixes only produce their values on -certain timesteps, which must be compatible with Nevery, else an -error results. Users can also write code for their own fix styles and -add them to LAMMPS. +appended, the per-atom vector calculated by the fix is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +Nevery, else an error results. Users can also write code for their +own fix styles and add them to LAMMPS.

    If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Variables of style diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 9a139b544d..80e0d6de9d 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -24,11 +24,11 @@ one or more values can be listed :l value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) density/number, density/mass = number or mass density - c_ID = per-atom scalar value calculated by a compute with ID - c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID - f_ID = per-atom scalar value calculated by a fix with ID - f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID - v_name = per-atom value calculated by an atom-style variable with name :pre + c_ID = per-atom vector value calculated by a compute with ID + c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector value calculated by a fix with ID + f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name :pre zero or more keyword/arg pairs may be appended :l keyword = {norm} or {units} or {file} or {ave} :l @@ -140,19 +140,19 @@ output. If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the compute is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. +appended, the per-atom vector calculated by the compute is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is -appended, the per-atom scalar calculated by the fix is used. If a -bracketed term is appended, the Nth vector per-atom value calculated -by the fix is used. Note that some fixes only produce their values on -certain timesteps, which must be compatible with {Nevery}, else an -error results. Users can also write code for their own fix styles and -"add them to LAMMPS"_Section_modify.html. +appended, the per-atom vector calculated by the fix is used. If a +bracketed term is appended, the Nth column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +{Nevery}, else an error results. Users can also write code for their +own fix styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Variables of style diff --git a/doc/fix_coord_original.html b/doc/fix_coord_original.html index e3328f5ece..159356f266 100644 --- a/doc/fix_coord_original.html +++ b/doc/fix_coord_original.html @@ -72,9 +72,9 @@ uninterrupted fashion.

    None of the fix_modify options are relevant to this fix.

    -

    This fix produces a per-atom vector which can be accessed by various -output commands. The length of the vector -for each atom is 3, and the components store the original unwrapped +

    This fix produces a per-atom array which can be accessed by various +output commands. The number of columns +for each atom is 3, and the columns store the original unwrapped x,y,z coords of each atom. The per-atom values be accessed on any timestep.

    diff --git a/doc/fix_coord_original.txt b/doc/fix_coord_original.txt index ed5a47a96e..94540eb5b0 100644 --- a/doc/fix_coord_original.txt +++ b/doc/fix_coord_original.txt @@ -64,9 +64,9 @@ uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. -This fix produces a per-atom vector which can be accessed by various -"output commands"_Section_howto.html#4_15. The length of the vector -for each atom is 3, and the components store the original unwrapped +This fix produces a per-atom array which can be accessed by various +"output commands"_Section_howto.html#4_15. The number of columns +for each atom is 3, and the columns store the original unwrapped x,y,z coords of each atom. The per-atom values be accessed on any timestep. diff --git a/doc/fix_move.html b/doc/fix_move.html index c1de476736..c3f69b0a4a 100644 --- a/doc/fix_move.html +++ b/doc/fix_move.html @@ -183,9 +183,9 @@ uninterrupted fashion.

    None of the fix_modify options are relevant to this fix.

    -

    This fix produces a per-atom vector which can be accessed by various -output commands. The length of the vector -for each atom is 3, and the components store the original unwrapped +

    This fix produces a per-atom array which can be accessed by various +output commands. The number of columns +for each atom is 3, and the columns store the original unwrapped x,y,z coords of each atom. The per-atom values be accessed on any timestep.

    diff --git a/doc/fix_move.txt b/doc/fix_move.txt index ea000fc0bf..cf589f3f16 100644 --- a/doc/fix_move.txt +++ b/doc/fix_move.txt @@ -174,9 +174,9 @@ uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. -This fix produces a per-atom vector which can be accessed by various -"output commands"_Section_howto.html#4_15. The length of the vector -for each atom is 3, and the components store the original unwrapped +This fix produces a per-atom array which can be accessed by various +"output commands"_Section_howto.html#4_15. The number of columns +for each atom is 3, and the columns store the original unwrapped x,y,z coords of each atom. The per-atom values be accessed on any timestep. diff --git a/doc/variable.html b/doc/variable.html index 395ceaefce..ce1cfe7031 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -342,8 +342,8 @@ compute. N is a global atom ID (positive integer). c_ID[2] vector component of a global compute c_ID[N] single atom's scalar value of a per-atom compute c_ID[N][M] single atom's vector component of a per-atom compute -c_ID[] per-atom scalar from a per-atom compute -c_ID[][M] per-atom vector component from a per-atom compute +c_ID[] per-atom vector from a per-atom compute +c_ID[][M] column of per-atom array from a per-atom compute

    Fix references access one or more quantities calculated by a diff --git a/doc/variable.txt b/doc/variable.txt index 54d6e44541..1d3e6d2037 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -337,8 +337,8 @@ c_ID: scalar value of a global compute c_ID\[2\]: vector component of a global compute c_ID\[N\]: single atom's scalar value of a per-atom compute c_ID\[N\]\[M\]: single atom's vector component of a per-atom compute -c_ID\[\]: per-atom scalar from a per-atom compute -c_ID\[\]\[M\]: per-atom vector component from a per-atom compute :tb(s=:) +c_ID\[\]: per-atom vector from a per-atom compute +c_ID\[\]\[M\]: column of per-atom array from a per-atom compute :tb(s=:) Fix references access one or more quantities calculated by a "fix"_fix.html. The ID in the reference should be replaced by the diff --git a/lib/atc/ATC_Transfer.cpp b/lib/atc/ATC_Transfer.cpp index a10026de64..1934fc1543 100644 --- a/lib/atc/ATC_Transfer.cpp +++ b/lib/atc/ATC_Transfer.cpp @@ -44,7 +44,7 @@ namespace ATC { scalarFlag_(0), vectorFlag_(0), sizeVector_(0), - scalarVectorFreq_(0), + globalFreq_(0), extScalar_(0), extVector_(0), extList_(NULL), diff --git a/lib/atc/ATC_Transfer.h b/lib/atc/ATC_Transfer.h index e41d218f21..c1c43ac839 100644 --- a/lib/atc/ATC_Transfer.h +++ b/lib/atc/ATC_Transfer.h @@ -201,7 +201,7 @@ namespace ATC { int scalar_flag() const {return scalarFlag_;} int vector_flag() const {return vectorFlag_;} int size_vector() const {return sizeVector_;} - int scalar_vector_freq() const {return scalarVectorFreq_;}; + int global_freq() const {return globalFreq_;}; int extscalar() const {return extScalar_;}; int extvector() const {return extVector_;}; int * extlist() {return extList_;}; @@ -716,7 +716,7 @@ namespace ATC { int scalarFlag_; // 0/1 if compute_scalar() function exists int vectorFlag_; // 0/1 if compute_vector() function exists int sizeVector_; // N = size of global vector - int scalarVectorFreq_; // frequency compute s/v data is available at + int globalFreq_; // frequency global data is available at int extScalar_; // 0/1 if scalar is intensive/extensive int extVector_; // 0/1/-1 if vector is all int/ext/extlist int *extList_; // list of 0/1 int/ext for each vec component diff --git a/lib/atc/ATC_TransferThermal.cpp b/lib/atc/ATC_TransferThermal.cpp index 2986a1597b..6dd5b981d6 100644 --- a/lib/atc/ATC_TransferThermal.cpp +++ b/lib/atc/ATC_TransferThermal.cpp @@ -43,7 +43,7 @@ namespace ATC { // output[2] = average temperature vectorFlag_ = 1; sizeVector_ = 2; - scalarVectorFreq_ = 1; + globalFreq_ = 1; extVector_ = 1; if (extrinsicModel != NO_MODEL) sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_); diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 2965aa7eee..33d479c268 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -557,7 +557,7 @@ double** LammpsInterface::compute_vector_data(const char* tag) cmpt->compute_peratom(); cmpt->invoked_flag |= INVOKED_PERATOM; } - return cmpt->vector_atom; + return cmpt->array_atom; } double* LammpsInterface::compute_scalar_data(const char* tag) @@ -567,13 +567,13 @@ double* LammpsInterface::compute_scalar_data(const char* tag) cmpt->compute_peratom(); cmpt->invoked_flag |= INVOKED_PERATOM; } - return cmpt->scalar_atom; + return cmpt->vector_atom; } int LammpsInterface::compute_ncols(const char* tag) { int icompute = find_compute(tag); - int ncols = lammps_->modify->compute[icompute]->size_peratom; + int ncols = lammps_->modify->compute[icompute]->size_peratom_cols; if (ncols == 0) ncols = 1; // oddity of lammps, used as flag for scalar return ncols; } @@ -615,7 +615,7 @@ double * LammpsInterface::atomPE_compute(void) { if (atomPE_) { atomPE_->compute_peratom(); - return atomPE_->scalar_atom; + return atomPE_->vector_atom; } else { return NULL;