From 19267785f56afe5b0f835d7d04b0722bdf80e608 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 2 May 2014 21:47:08 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11906 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_python.html | 10 +++++----- doc/Section_python.txt | 10 +++++----- doc/compute_property_atom.html | 7 ++++++- doc/compute_property_atom.txt | 7 ++++++- doc/compute_vacf.html | 2 +- doc/compute_vacf.txt | 2 +- doc/dump.html | 19 +++++++++++-------- doc/dump.txt | 19 +++++++++++-------- doc/dump_modify.html | 2 +- doc/dump_modify.txt | 2 +- doc/fix_restrain.html | 2 +- doc/fix_restrain.txt | 2 +- doc/pair_coul_diel.html | 2 ++ doc/pair_coul_diel.txt | 1 + doc/pair_lj_long.html | 4 ++-- doc/pair_lj_long.txt | 4 ++-- 16 files changed, 57 insertions(+), 38 deletions(-) diff --git a/doc/Section_python.html b/doc/Section_python.html index 6fcc0f0e8b..82addb5052 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -545,12 +545,12 @@ this: natoms = lmp.get_natoms() n3 = 3*natoms x = (n3*c_double)() -x0 = x coord of atom with ID 1 -x1 = y coord of atom with ID 1 -x2 = z coord of atom with ID 1 -x3 = x coord of atom with ID 2 +x[0] = x coord of atom with ID 1 +x[1] = y coord of atom with ID 1 +x[2] = z coord of atom with ID 1 +x[3] = x coord of atom with ID 2 ... -xn3-1 = z coord of atom with ID natoms +x[n3-1] = z coord of atom with ID natoms lmp.scatter_coords("x",1,3,x)

Alternatively, you can just change values in the vector returned by diff --git a/doc/Section_python.txt b/doc/Section_python.txt index 872a4c68bf..7be127ef9f 100644 --- a/doc/Section_python.txt +++ b/doc/Section_python.txt @@ -540,12 +540,12 @@ from ctypes import * natoms = lmp.get_natoms() n3 = 3*natoms x = (n3*c_double)() -x[0] = x coord of atom with ID 1 -x[1] = y coord of atom with ID 1 -x[2] = z coord of atom with ID 1 -x[3] = x coord of atom with ID 2 +x\[0\] = x coord of atom with ID 1 +x\[1\] = y coord of atom with ID 1 +x\[2\] = z coord of atom with ID 1 +x\[3\] = x coord of atom with ID 2 ... -x[n3-1] = z coord of atom with ID natoms +x\[n3-1\] = z coord of atom with ID natoms lmp.scatter_coords("x",1,3,x) :pre Alternatively, you can just change values in the vector returned by diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index 75674c3915..bbf71ff36d 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -34,6 +34,7 @@ corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, + nbonds, i_name, d_name 

      id = atom ID
@@ -60,7 +61,8 @@
       ervel = electron radial velocity
       erforce = electron radial force
       end12x, end12y, end12z = end points of line segment
-      coner123x, corner123y, corner123z = corner points of triangle
+      corner123x, corner123y, corner123z = corner points of triangle
+      nbonds = number of bonds
       i_name = custom integer vector with name
       d_name = custom integer vector with name
@@ -111,6 +113,9 @@ line segment particles and define the end points of each line segment. corner2z, corner3x, corner3y, corner3z, are defined for triangular particles and define the corner points of each triangle.

+

nbonds is available for all molecular atom styles and refers to +the number of explicit bonds attached to an atom. +

The i_name and d_name attributes refer to custom integer and floating-point properties that have been added to each atom via the fix property/atom command. When that command diff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt index 558d72d76e..0ae271ad25 100644 --- a/doc/compute_property_atom.txt +++ b/doc/compute_property_atom.txt @@ -28,6 +28,7 @@ input = one or more atom attributes :l corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, + nbonds, i_name, d_name :pre id = atom ID mol = molecule ID @@ -53,7 +54,8 @@ input = one or more atom attributes :l ervel = electron radial velocity erforce = electron radial force end12x, end12y, end12z = end points of line segment - coner123x, corner123y, corner123z = corner points of triangle + corner123x, corner123y, corner123z = corner points of triangle + nbonds = number of bonds i_name = custom integer vector with name d_name = custom integer vector with name :pre :ule @@ -103,6 +105,9 @@ line segment particles and define the end points of each line segment. {corner2z}, {corner3x}, {corner3y}, {corner3z}, are defined for triangular particles and define the corner points of each triangle. +{nbonds} is available for all molecular atom styles and refers to +the number of explicit bonds attached to an atom. + The {i_name} and {d_name} attributes refer to custom integer and floating-point properties that have been added to each atom via the "fix property/atom"_fix_property_atom.html command. When that command diff --git a/doc/compute_vacf.html b/doc/compute_vacf.html index a46344aa7d..be1fac7cf0 100644 --- a/doc/compute_vacf.html +++ b/doc/compute_vacf.html @@ -43,7 +43,7 @@ coefficient of the diffusing atoms. This can be computed in the following manner, using the variable trap() function: 

compute         2 all vacf
-fix             5 all vector 1 c_24
+fix             5 all vector 1 c_2[4]
 variable        diff equal dt*trap(f_5)
 thermo_style    custom step v_diff
diff --git a/doc/compute_vacf.txt b/doc/compute_vacf.txt index bb1e157a2a..31b288d967 100644 --- a/doc/compute_vacf.txt +++ b/doc/compute_vacf.txt @@ -40,7 +40,7 @@ coefficient of the diffusing atoms. This can be computed in the following manner, using the "variable trap()"_variable.html function: compute 2 all vacf -fix 5 all vector 1 c_2[4] +fix 5 all vector 1 c_2\[4\] variable diff equal dt*trap(f_5) thermo_style custom step v_diff :pre diff --git a/doc/dump.html b/doc/dump.html index 3d0cbb18ef..8b63b05e2a 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -25,7 +25,7 @@
  • group-ID = ID of the group of atoms to be dumped -
  • style = atom or atom/mpiio or cfg or dcd or xtc or xyz or xyz/mpiio or image or molfile or local or custom or custom/mpiio +
  • style = atom or atom/mpiio or cfg or dcd or xtc or xyz or xyz/mpiio or image or movie or molfile or local or custom or custom/mpiio
  • N = dump every this many timesteps @@ -44,6 +44,8 @@ 
      image args = discussed on dump image doc page
    +
      movie args = discussed on dump image doc page 
+
      molfile args = discussed on dump molfile doc page 
 
      local args = list of local attributes
@@ -105,19 +107,20 @@ dump 2 subgroup atom 50 dump.run.mpiio.bin
 dump 4a all custom 100 dump.myforce.* id type x y vx fx
 dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
 dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress2
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
 dump 1 all xtc 1000 file.xtc
 dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce

    Description:

    Dump a snapshot of atom quantities to one or more files every N -timesteps in one of several styles. The image style is the -exception; it creates a JPG or PPM image file of the atom -configuration every N timesteps, as discussed on the dump -image doc page. The timesteps on which dump output -is written can also be controlled by a variable; see the dump_modify -every command for details. +timesteps in one of several styles. The image and movie styles are +the exception: the image style renders a JPG, PNG, or PPM image file +of the atom configuration every N timesteps while the movie style +combines and compresses them into a movie file; both are discussed in +detail on the dump image doc page. The timesteps on +which dump output is written can also be controlled by a variable. +See the dump_modify every command.

    Only information for atoms in the specified group is dumped. The dump_modify thresh and region commands can also diff --git a/doc/dump.txt b/doc/dump.txt index b02f09c5f5..a0c8141092 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -17,7 +17,7 @@ dump ID group-ID style N file args :pre ID = user-assigned name for the dump :ulb,l group-ID = ID of the group of atoms to be dumped :l -style = {atom} or {atom/mpiio} or {cfg} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {molfile} or {local} or {custom} or {custom/mpiio} :l +style = {atom} or {atom/mpiio} or {cfg} or {dcd} or {xtc} or {xyz} or {xyz/mpiio} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/mpiio} :l N = dump every this many timesteps :l file = name of file to write dump info to :l args = list of arguments for a particular style :l @@ -31,6 +31,8 @@ args = list of arguments for a particular style :l {image} args = discussed on "dump image"_dump_image.html doc page :pre + {movie} args = discussed on "dump image"_dump_image.html doc page :pre + {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page :pre {local} args = list of local attributes @@ -91,19 +93,20 @@ dump 2 subgroup atom 50 dump.run.mpiio.bin dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz -dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] +dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress\[2\] dump 1 all xtc 1000 file.xtc dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre [Description:] Dump a snapshot of atom quantities to one or more files every N -timesteps in one of several styles. The {image} style is the -exception; it creates a JPG or PPM image file of the atom -configuration every N timesteps, as discussed on the "dump -image"_dump_image.html doc page. The timesteps on which dump output -is written can also be controlled by a variable; see the "dump_modify -every"_dump_modify.html command for details. +timesteps in one of several styles. The {image} and {movie} styles are +the exception: the {image} style renders a JPG, PNG, or PPM image file +of the atom configuration every N timesteps while the {movie} style +combines and compresses them into a movie file; both are discussed in +detail on the "dump image"_dump_image.html doc page. The timesteps on +which dump output is written can also be controlled by a variable. +See the "dump_modify every"_dump_modify.html command. Only information for atoms in the specified group is dumped. The "dump_modify thresh and region"_dump_modify.html commands can also diff --git a/doc/dump_modify.html b/doc/dump_modify.html index 19c7f21277..0a20b7a451 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -282,7 +282,7 @@ dump file as a (large) integer, then you need to use an appropriate format. For example, these commands: 

    compute     1 all property/local batom1 batom2
-dump        1 all local 100 tmp.bonds index c_11 c_12
+dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
 dump_modify 1 format "%d %0.0f %0.0f"

    will output the two atom IDs for atoms in each bond as integers. If diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index 84018f00ca..12bd61f97d 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -270,7 +270,7 @@ dump file as a (large) integer, then you need to use an appropriate format. For example, these commands: compute 1 all property/local batom1 batom2 -dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] +dump 1 all local 100 tmp.bonds index c_1\[1\] c_1\[2\] dump_modify 1 format "%d %0.0f %0.0f" :pre will output the two atom IDs for atoms in each bond as integers. If diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html index 8cdb789a52..6c0f498fab 100644 --- a/doc/fix_restrain.html +++ b/doc/fix_restrain.html @@ -31,7 +31,7 @@ atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom Kstart,Kstop = restraint coefficients at start/end of run (energy units) theta0 = equilibrium angle theta (degrees) - bond args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order Kstart,Kstop = restraint coefficients at start/end of run (energy units) phi0 = equilibrium dihedral angle phi (degrees) diff --git a/doc/fix_restrain.txt b/doc/fix_restrain.txt index e91a8ebeee..3518e3ee43 100644 --- a/doc/fix_restrain.txt +++ b/doc/fix_restrain.txt @@ -24,7 +24,7 @@ keyword = {bond} or {angle} or {dihedral} :l atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom Kstart,Kstop = restraint coefficients at start/end of run (energy units) theta0 = equilibrium angle theta (degrees) - {bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order Kstart,Kstop = restraint coefficients at start/end of run (energy units) phi0 = equilibrium dihedral angle phi (degrees) :pre diff --git a/doc/pair_coul_diel.html b/doc/pair_coul_diel.html index c7ce1de683..a5f97bce47 100644 --- a/doc/pair_coul_diel.html +++ b/doc/pair_coul_diel.html @@ -11,6 +11,8 @@

    pair_style coul/diel command

    +

    pair_style coul/diel/omp command +

    Syntax: 

    pair_style coul/diel cutoff 
diff --git a/doc/pair_coul_diel.txt b/doc/pair_coul_diel.txt
index 21cac35bf5..95112597f7 100644
--- a/doc/pair_coul_diel.txt
+++ b/doc/pair_coul_diel.txt
@@ -7,6 +7,7 @@
 :line
 
 pair_style coul/diel command :h3
+pair_style coul/diel/omp command :h3
 
 [Syntax:]
 
diff --git a/doc/pair_lj_long.html b/doc/pair_lj_long.html
index c4c62c459c..350c2a2212 100644
--- a/doc/pair_lj_long.html
+++ b/doc/pair_lj_long.html
@@ -34,7 +34,7 @@
       off = omit Coulombic term
     cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
+  lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
     flag_lj = long or cut
       long = use Kspace long-range summation for dispersion 1/r^6 term
       cut = use a cutoff
@@ -83,7 +83,7 @@ settings.  The In 't Veld paper has more details on when i
 appropriate to include long-range 1/r^6 interactions, using this
 potential.
 
    
-
    Style lj/cut/tip4p/long implements the TIP4P water model of
+
    Style lj/long/tip4p/long implements the TIP4P water model of
 (Jorgensen), which introduces a massless site located a
 short distance away from the oxygen atom along the bisector of the HOH
 angle.  The atomic types of the oxygen and hydrogen atoms, the bond
diff --git a/doc/pair_lj_long.txt b/doc/pair_lj_long.txt
index 80f4283083..a1f271033a 100644
--- a/doc/pair_lj_long.txt
+++ b/doc/pair_lj_long.txt
@@ -27,7 +27,7 @@ args = list of arguments for a particular style :ul
       {off} = omit Coulombic term
     cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {lj/cut/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
+  {lj/long/tip4p/long} args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
     flag_lj = {long} or {cut}
       {long} = use Kspace long-range summation for dispersion 1/r^6 term
       {cut} = use a cutoff
@@ -76,7 +76,7 @@ settings.  The "In 't Veld"_#Veld paper has more details on when it is
 appropriate to include long-range 1/r^6 interactions, using this
 potential.
 
-Style {lj/cut/tip4p/long} implements the TIP4P water model of
+Style {lj/long/tip4p/long} implements the TIP4P water model of
 "(Jorgensen)"_#Jorgensen, which introduces a massless site located a
 short distance away from the oxygen atom along the bisector of the HOH
 angle.  The atomic types of the oxygen and hydrogen atoms, the bond