From b4ad6888a0a0fca2a2ab6b972270fa9876ad6d9e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 21 Jul 2015 23:11:53 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13663 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 7 ++--- doc/Section_commands.txt | 5 +++- doc/Section_packages.html | 19 ++++++++++++++ doc/Section_packages.txt | 19 ++++++++++++++ doc/compute_saed.html | 25 ++++++++++-------- doc/compute_saed.txt | 22 +++++++++------- doc/compute_xrd.html | 54 +++++++++++++++++++++------------------ doc/compute_xrd.txt | 51 +++++++++++++++++++----------------- doc/fix_ave_histo.html | 18 ++++++------- doc/fix_ave_histo.txt | 18 ++++++------- doc/fix_saed_vtk.html | 14 +++++----- doc/fix_saed_vtk.txt | 6 ++--- 12 files changed, 159 insertions(+), 99 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 87bc66cad9..550da65be9 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -436,8 +436,8 @@ package. imdipilangevin/efflb/fluidlb/momentumlb/pc lb/rigid/pc/spherelb/viscousmesomeso/stationarynph/effnpt/eff nve/effnvt/effnvt/sllod/effphononpimdqeq/reax -qmmmreax/c/bondsreax/c/speciessmdtemp/rescale/effti/rs -ti/springttm/mod +qmmmreax/c/bondsreax/c/speciessaed/vtksmdtemp/rescale/eff +ti/rsti/springttm/mod
@@ -472,7 +472,8 @@ package.

- +
ackland/atombasal/atomfepke/effke/atom/effmeso_e/atom
meso_rho/atommeso_t/atomtemp/efftemp/deform/efftemp/region/efftemp/rotate +
meso_rho/atommeso_t/atomsaedtemp/efftemp/deform/efftemp/region/eff
temp/rotatexrd
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 8d026e861a..b6bcd79dee 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -624,6 +624,7 @@ package"_Section_start.html#start_3. "qmmm"_fix_qmmm.html, "reax/c/bonds"_fix_reax_bonds.html, "reax/c/species"_fix_reaxc_species.html, +"saed/vtk"_fix_saed_vtk.html, "smd"_fix_smd.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/rs"_fix_ti_rs.html, @@ -721,10 +722,12 @@ package"_Section_start.html#start_3. "meso_e/atom"_compute_meso_e_atom.html, "meso_rho/atom"_compute_meso_rho_atom.html, "meso_t/atom"_compute_meso_t_atom.html, +"saed"_compute_saed.html, "temp/eff"_compute_temp_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html, "temp/region/eff"_compute_temp_region_eff.html, -"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c) +"temp/rotate"_compute_temp_rotate.html, +"xrd"_compute_xrd.html :tb(c=6,ea=c) :line diff --git a/doc/Section_packages.html b/doc/Section_packages.html index ed2125d604..9295269d8f 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -126,6 +126,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries. USER-CG-CMM coarse-graining model Axel Kohlmeyer (Temple U) pair_style lj/sdk USER/cg-cmm cg - USER-COLVARS collective variables Fiorin & Henin & Kohlmeyer (3) fix colvars USER/colvars colvars lib/colvars USER-CUDA NVIDIA GPU styles Christian Trott (U Tech Ilmenau) Section accelerate USER/cuda - lib/cuda +USER-DIFFRACTION virutal x-ray and electron diffraction Shawn Coleman (ARL)compute xrd USER/diffraction - - USER-EFF electron force field Andres Jaramillo-Botero (Caltech) pair_style eff/cut USER/eff eff - USER-FEP free energy perturbation Agilio Padua (U Blaise Pascal Clermont-Ferrand) compute fep USER/fep - - USER-INTEL Vectorized CPU and Intel(R) coprocessor styles W. Michael Brown (Intel) Section accelerate examples/intel - - @@ -336,6 +337,24 @@ tu-ilmenau.de). Contact him directly if you have questions.

+

USER-DIFFRACTION package +

+

This package contains the commands neeed to calculate x-ray and +electron diffraction intensities based on kinematic diffraction +theory. +

+

See these doc pages and their related commands to get started: +

+ +

The person who created this package is Shawn P. Coleman +(shawn.p.coleman8.ctr at mail.mil) while at the University of +Arkansas. Contact him directly if you have questions. +

+
+

USER-EFF package

This package contains a LAMMPS implementation of the electron Force diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 697339b662..13182ac008 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -118,6 +118,7 @@ USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpm USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, - USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda +USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, - USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - @@ -323,6 +324,24 @@ tu-ilmenau.de). Contact him directly if you have questions. :line +USER-DIFFRACTION package :h4 + +This package contains the commands neeed to calculate x-ray and +electron diffraction intensities based on kinematic diffraction +theory. + +See these doc pages and their related commands to get started: + +"compute xrd"_compute_xrd.html +"compute saed"_compute_saed.html +"fix saed/vtk"_fix_saed_vtk.html :ul + +The person who created this package is Shawn P. Coleman +(shawn.p.coleman8.ctr at mail.mil) while at the University of +Arkansas. Contact him directly if you have questions. + +:line + USER-EFF package :h4 This package contains a LAMMPS implementation of the electron Force diff --git a/doc/compute_saed.html b/doc/compute_saed.html index 178de056b4..c8f4ad0cec 100644 --- a/doc/compute_saed.html +++ b/doc/compute_saed.html @@ -21,8 +21,7 @@

  • lambda = wavelength of incident radiation (length units) -
  • type1 type2 ... typeN = chemical symbol of each atom type (see valid -options below) +
  • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
  • zero or more keyword/value pairs may be appended @@ -46,9 +45,9 @@ options below)

    Examples:

    -

    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo -

    +
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo 
+
    fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
 fix saed/vtk 1 1 1 c_2 file Ni_000.saed
    @@ -71,8 +70,11 @@ position of each atom, fj are atomic scattering factors.

    Diffraction intensities are calculated on a three-dimensional mesh of reciprocal lattice nodes. The mesh spacing is defined either (I) by -the entire simulation domain or (II) manually using selected values. +the entire simulation domain or (II) manually using selected values as +shown in the 2D diagram below.

    +
    +

    For a mesh defined by the simulation domain, a rectilinear grid is constructed with spacing c*inv(A) along each reciprocal lattice axis. Where A are the vectors corresponding to the edges of the @@ -100,8 +102,11 @@ increase the cost of computation. Otherwise, Zone parameters will denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an intersecting Ewald sphere. Diffraction intensities will only be computed at the intersection of the reciprocal lattice mesh and a -dR_Ewald thick surface of the Ewald sphere. +dR_Ewald thick surface of the Ewald sphere. See the example 3D +intestiety data and the intersection of a 010 zone axis in the below image.

    +
    +

    The atomic scattering factors, fj, accounts for the reduction in diffraction intensity due to Compton scattering. Compute saed uses analytical approximations of the atomic scattering factors that vary @@ -159,12 +164,12 @@ options.

    Related commands:

    -

    fix saed_vtk -compute xrd +

    fix saed_vtk, compute xrd

    Default:

    -

    The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = 0.01 +

    The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = +0.01.

    diff --git a/doc/compute_saed.txt b/doc/compute_saed.txt index d2aaae2056..9bf628f6f2 100644 --- a/doc/compute_saed.txt +++ b/doc/compute_saed.txt @@ -15,8 +15,7 @@ compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l saed = style name of this compute command :l lambda = wavelength of incident radiation (length units) :l -type1 type2 ... typeN = chemical symbol of each atom type (see valid -options below) :l +type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l zero or more keyword/value pairs may be appended :l keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l @@ -38,7 +37,7 @@ keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l [Examples:] compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo +compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre @@ -61,7 +60,10 @@ position of each atom, fj are atomic scattering factors. Diffraction intensities are calculated on a three-dimensional mesh of reciprocal lattice nodes. The mesh spacing is defined either (I) by -the entire simulation domain or (II) manually using selected values. +the entire simulation domain or (II) manually using selected values as +shown in the 2D diagram below. + +:c,image(JPG/saed_mesh_small.jpg,saed_mesh.jpg) For a mesh defined by the simulation domain, a rectilinear grid is constructed with spacing {c}*inv(A) along each reciprocal lattice @@ -90,7 +92,10 @@ increase the cost of computation. Otherwise, {Zone} parameters will denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an intersecting Ewald sphere. Diffraction intensities will only be computed at the intersection of the reciprocal lattice mesh and a -{dR_Ewald} thick surface of the Ewald sphere. +{dR_Ewald} thick surface of the Ewald sphere. See the example 3D +intestiety data and the intersection of a [010] zone axis in the below image. + +:c,image(JPG/saed_ewald_intersect_small.jpg,saed_ewald_intersect.jpg) The atomic scattering factors, fj, accounts for the reduction in diffraction intensity due to Compton scattering. Compute saed uses @@ -150,12 +155,12 @@ The compute_saed command does not work for triclinic cells. [Related commands:] -"fix saed_vtk"_fix_saed_vtk.html -"compute xrd"_compute_xrd.html +"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html [Default:] -The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = 0.01 +The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = +0.01. :line @@ -170,4 +175,3 @@ Volume C: Mathematical and Chemical Tables, 554-95 (2004). :link(Fox) [(Fox)] Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 (1989). - diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index bbcd1ddfab..253f936a21 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -21,8 +21,7 @@
  • lambda = wavelength of incident radiation (length units) -
  • type1 type2 ... typeN = chemical symbol of each atom type (see valid -options below) +
  • type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
  • zero or more keyword/value pairs may be appended @@ -44,12 +43,12 @@ options below)

    Examples:

    -

    compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo +

    compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo 
 compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual 
-
    
-
    fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_11 mode vector weights c_12 file Rad2Theta.xrd
-fix 2 all ave/histo 1 1 1 10 100 250 c_21 mode vector weights c_22 file Deg2Theta.xrd
-
    
+
    +
    fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1[1] mode vector weights c_1[2] file Rad2Theta.xrd
+fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd 
+

    Description: @@ -78,8 +77,11 @@ the LP switch.

    Diffraction intensities are calculated on a three-dimensional mesh of reciprocal lattice nodes. The mesh spacing is defined either (I) -by the entire simulation domain or (II) manually using selected values. +by the entire simulation domain or (II) manually using selected values as +shown in the 2D diagram below.

    +
    +

    For a mesh defined by the simulation domain, a rectilinear grid is constructed with spacing c*inv(A) along each reciprocal lattice axis. Where A are the vectors corresponding to the edges of the @@ -89,23 +91,24 @@ average of the (inversed) box lengths with periodic boundary conditions. Meshes defined by the simulation domain must contain at least one periodic boundary.

    -

    If the manual flag is included, the mesh of reciprocal lattice nodes -will defined using the c values for the spacing along each reciprocal -lattice axis. Note that manual mapping of the reciprocal space mesh is -good for comparing diffraction results from multiple simulations; however -it can reduce the likelihood that Bragg reflections will be satisfied -unless small spacing parameters <0.05 Angstrom^(-1) are implemented. -Meshes with manual spacing do not require a periodic boundary. +

    If the manual flag is included, the mesh of reciprocal lattice nodes +will defined using the c values for the spacing along each +reciprocal lattice axis. Note that manual mapping of the reciprocal +space mesh is good for comparing diffraction results from multiple +simulations; however it can reduce the likelihood that Bragg +reflections will be satisfied unless small spacing parameters (< 0.05 +Angstrom^(-1)) are implemented. Meshes with manual spacing do not +require a periodic boundary.

    -

    The limits of the reciprocal lattice mesh are determined by range of -scattering angles explored. The 2Theta parameters allows the user to -reduce the scattering angle range to only the region of interest which -reduces the cost of the computation. +

    The limits of the reciprocal lattice mesh are determined by range of +scattering angles explored. The 2Theta parameters allows the user +to reduce the scattering angle range to only the region of interest +which reduces the cost of the computation.

    -

    The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute xrd uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. +

    The atomic scattering factors, fj, accounts for the reduction in +diffraction intensity due to Compton scattering. Compute xrd uses +analytical approximations of the atomic scattering factors that vary +for each atom type (type1 type2 ... typeN) and angle of diffraction. The analytic approximation is computed using the formula (Colliex):

    @@ -183,12 +186,13 @@ options.

    Related commands:

    -

    fix ave/histo +

    fix ave/histo, compute saed

    Default:

    -

    The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, no manual flag, no echo flag +

    The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, +no manual flag, no echo flag.

    diff --git a/doc/compute_xrd.txt b/doc/compute_xrd.txt index 4e03ef5709..486fd22951 100644 --- a/doc/compute_xrd.txt +++ b/doc/compute_xrd.txt @@ -15,8 +15,7 @@ compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l xrd = style name of this compute command :l lambda = wavelength of incident radiation (length units) :l -type1 type2 ... typeN = chemical symbol of each atom type (see valid -options below) :l +type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l zero or more keyword/value pairs may be appended :l keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l @@ -36,10 +35,10 @@ keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l [Examples:] compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo -compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual +compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre -fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1[1] mode vector weights c_1[2] file Rad2Theta.xrd -fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd +fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1\[1\] mode vector weights c_1\[2\] file Rad2Theta.xrd +fix 2 all ave/histo 1 1 1 10 100 250 c_2\[1\] mode vector weights c_2\[2\] file Deg2Theta.xrd :pre :pre @@ -66,7 +65,11 @@ the {LP} switch. Diffraction intensities are calculated on a three-dimensional mesh of reciprocal lattice nodes. The mesh spacing is defined either (I) -by the entire simulation domain or (II) manually using selected values. +by the entire simulation domain or (II) manually using selected values as +shown in the 2D diagram below. + +:c,image(JPG/xrd_mesh_small.jpg,xrd_mesh.jpg) + For a mesh defined by the simulation domain, a rectilinear grid is constructed with spacing {c}*inv(A) along each reciprocal lattice @@ -77,23 +80,24 @@ average of the (inversed) box lengths with periodic boundary conditions. Meshes defined by the simulation domain must contain at least one periodic boundary. -If the {manual} flag is included, the mesh of reciprocal lattice nodes -will defined using the {c} values for the spacing along each reciprocal -lattice axis. Note that manual mapping of the reciprocal space mesh is -good for comparing diffraction results from multiple simulations; however -it can reduce the likelihood that Bragg reflections will be satisfied -unless small spacing parameters [<0.05 Angstrom^(-1)] are implemented. -Meshes with manual spacing do not require a periodic boundary. +If the {manual} flag is included, the mesh of reciprocal lattice nodes +will defined using the {c} values for the spacing along each +reciprocal lattice axis. Note that manual mapping of the reciprocal +space mesh is good for comparing diffraction results from multiple +simulations; however it can reduce the likelihood that Bragg +reflections will be satisfied unless small spacing parameters (< 0.05 +Angstrom^(-1)) are implemented. Meshes with manual spacing do not +require a periodic boundary. -The limits of the reciprocal lattice mesh are determined by range of -scattering angles explored. The {2Theta} parameters allows the user to -reduce the scattering angle range to only the region of interest which -reduces the cost of the computation. +The limits of the reciprocal lattice mesh are determined by range of +scattering angles explored. The {2Theta} parameters allows the user +to reduce the scattering angle range to only the region of interest +which reduces the cost of the computation. -The atomic scattering factors, fj, accounts for the reduction in -diffraction intensity due to Compton scattering. Compute xrd uses -analytical approximations of the atomic scattering factors that vary -for each atom type (type1 type2 ... typeN) and angle of diffraction. +The atomic scattering factors, fj, accounts for the reduction in +diffraction intensity due to Compton scattering. Compute xrd uses +analytical approximations of the atomic scattering factors that vary +for each atom type (type1 type2 ... typeN) and angle of diffraction. The analytic approximation is computed using the formula "(Colliex)"_#Colliex: @@ -172,12 +176,13 @@ The compute_xrd command does not work for triclinic cells. [Related commands:] -"fix ave/histo"_compute_ave_histo.html +"fix ave/histo"_compute_ave_histo.html, "compute saed"_compute_saed.html [Default:] -The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, no manual flag, no echo flag +The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, +no manual flag, no echo flag. :line diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html index 7533cc70a5..d941762f0b 100644 --- a/doc/fix_ave_histo.html +++ b/doc/fix_ave_histo.html @@ -66,7 +66,7 @@ string = text to print as 2nd line of output file title3 arg = string string = text to print as 3rd line of output file, only for vector mode - weights arg = c_ID, c_ID[N], f_ID, f_ID[N], v_name + weights arg = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID = scalar or vector calculated by a compute with ID c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID f_ID = scalar or vector calculated by a fix with ID @@ -294,14 +294,14 @@ describes the six values that are printed at the first of each section of output. The third describes the 4 values printed for each bin in the histogram.

    -

    If the weights keyword is specified, the fix will compute a weighted -histogram using per-bin weights specified by the weights argument. As -normal, the bin locations will be will be generated based off value1. -However, instead of each binned value contributing 1 to the bin -location, the contributing ammount is assigned the weights -argument. Only a single value1 and weights argument pair can be can be -used for each fix ave/histo. The length of value1 must match the -lenght of the weights arguemnt. +

    If the weights keyword is specified, the fix will generate a weighted +histogram using data from the assigned value1 and weights argument. +As normal, the bin locations will be will be generated based off value1. +However, instead of each binned value contributing 1 to the bin location, +the contributing ammount is assigned the weights argument. Only a single +value1 and weights argument pair can be can be used for each fix +ave/histo. The length of value1 must match the lenght of the weights +arguemnt.

    diff --git a/doc/fix_ave_histo.txt b/doc/fix_ave_histo.txt index a954c29325..d5d5c095a2 100644 --- a/doc/fix_ave_histo.txt +++ b/doc/fix_ave_histo.txt @@ -52,7 +52,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti string = text to print as 2nd line of output file {title3} arg = string string = text to print as 3rd line of output file, only for vector mode - {weights} arg = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name + {weights} arg = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name c_ID = scalar or vector calculated by a compute with ID c_ID\[I\] = Ith component of vector or Ith column of array calculated by a compute with ID f_ID = scalar or vector calculated by a fix with ID @@ -279,14 +279,14 @@ describes the six values that are printed at the first of each section of output. The third describes the 4 values printed for each bin in the histogram. -If the {weights} keyword is specified, the fix will compute a weighted -histogram using per-bin weights specified by the {weights} argument. As -normal, the bin locations will be will be generated based off value1. -However, instead of each binned value contributing 1 to the bin -location, the contributing ammount is assigned the weights -argument. Only a single value1 and weights argument pair can be can be -used for each fix ave/histo. The length of value1 must match the -lenght of the weights arguemnt. +If the {weights} keyword is specified, the fix will generate a weighted +histogram using data from the assigned value1 and weights argument. +As normal, the bin locations will be will be generated based off value1. +However, instead of each binned value contributing 1 to the bin location, +the contributing ammount is assigned the weights argument. Only a single +value1 and weights argument pair can be can be used for each fix +ave/histo. The length of value1 must match the lenght of the weights +arguemnt. :line diff --git a/doc/fix_saed_vtk.html b/doc/fix_saed_vtk.html index 55c15e8893..370ebe7856 100644 --- a/doc/fix_saed_vtk.html +++ b/doc/fix_saed_vtk.html @@ -42,9 +42,9 @@

    Examples:

    -

    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo -

    +
    compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo 
+
    fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
 fix saed/vtk 1 1 1 c_2 file Ni_000.saed
    @@ -69,11 +69,11 @@ specified values may represent calculations performed by saed computes which store their own "group" definitions.

    Fix saed/vtk is designed to work only with compute_saed -values. -

    -

    compute 3 top saed 0.0251 Al O -fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed +values, e.g.

    +
    compute 3 top saed 0.0251 Al O 
+fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed 
+

    The Nevery, Nrepeat, and Nfreq arguments specify on what diff --git a/doc/fix_saed_vtk.txt b/doc/fix_saed_vtk.txt index 67c940b192..1f048e9c3a 100644 --- a/doc/fix_saed_vtk.txt +++ b/doc/fix_saed_vtk.txt @@ -35,7 +35,7 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l [Examples:] compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo +compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre @@ -61,10 +61,10 @@ specified values may represent calculations performed by saed computes which store their own "group" definitions. Fix saed/vtk is designed to work only with "compute_saed"_compute_saed.txt -values. +values, e.g. compute 3 top saed 0.0251 Al O -fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed +fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed :pre :line